diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 0000000..3189fd0 --- /dev/null +++ b/AUTHORS @@ -0,0 +1,3 @@ +eFORGE was developed by Charles Breeze while on secondment at the European Bioinformatics Institute as part of the EpiTrain Initial Training Network. + +The code, webserver and database are currently maintained by Charles Breeze and Javier Herrero. diff --git a/COPYING b/COPYING new file mode 100644 index 0000000..94a0453 --- /dev/null +++ b/COPYING @@ -0,0 +1,621 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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CREATE AN EMPTY DATABASE + +Please refer to the help of init_db.pl for information about the different options + +rm eforge_1.2.db +perl init_db.pl --db_name eforge_1.2.db + +2. LOAD THE ARRAYS + +Please refer to the help of load_450k_array.pl for information about the different options + +perl load_450k_array.pl --work_dir input --db_name eforge_1.2.db +perl load_27k_array.pl --work_dir input --db_name eforge_1.2.db + +3. LOAD THE DATASETS + +Please refer to the help of load_dataset.pl for information about the different options + +perl load_dataset.pl --db_name eforge_1.2.db --tag erc --name 'Roadmap Epigenomics (2012 data) - DHS' --decode_file erc.decode --work_dir input/erc/ +perl load_dataset.pl --db_name eforge_1.2.db --tag encode --name 'ENCODE - DHS' --decode_file encode.decode --work_dir input/encode/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-DHS --name 'Consolidated Roadmap Epigenomics - DHS' --decode_file erc2.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K27me3 --name 'Consolidated Roadmap Epigenomics - H3K27me3' --decode_file erc2-H3K27me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K36me3 --name 'Consolidated Roadmap Epigenomics - H3K36me3' --decode_file erc2-H3K36me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K4me3 --name 'Consolidated Roadmap Epigenomics - H3K4me3' --decode_file erc2-H3K4me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K9me3 --name 'Consolidated Roadmap Epigenomics - H3K9me3' --decode_file erc2-H3K9me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K4me1 --name 'Consolidated Roadmap Epigenomics - H3K4me1' --decode_file erc2-H3K4me1.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3-all --name 'Consolidated Roadmap Epigenomics - All H3 marks' --decode_file erc2-H3-all.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag blueprint --name 'Blueprint - DHS' --decode_file blueprint.decode --work_dir input/blueprint/ + +4. MOVE THE DATABASE TO ITS FINAL LOCATION + +mv eforge_1.2.db .. diff --git a/database/blueprint.decode b/database/blueprint.decode new file mode 100644 index 0000000..eb41245 --- /dev/null +++ b/database/blueprint.decode @@ -0,0 +1,31 @@ +file lab datatype cell tissue shortcell individual acc url +BP_DG-75_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Sporadic_Burkitt_lymphoma Cell Line DG-75_Sporadic_Burkitt_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS/BP_DG-75_d01.DNase.hotspot_v3.20130819.bed.gz +S00C0J41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00C0J41.DNase.hotspot_v3.20141014.bed.gz +BP_U-266_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Multiple_myeloma Cell Line U-266_Multiple_myeloma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS/BP_U-266_d01.DNase.hotspot_v3.20130819.bed.gz +S00CR241.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00CR241.DNase.hotspot_v3.20141014.bed.gz +BP_Z-138_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Mantle_cell_lymphoma Cell Line Z-138_Mantle_cell_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS/BP_Z-138_d01.DNase.hotspot_v3.20130819.bed.gz +S00CS041.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00CS041.DNase.hotspot_v3.20141014.bed.gz +C0010K46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C0010K46.DNase.hotspot_v3.20130415.bed.gz +S00CTZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00CTZ41.DNase.hotspot_v3.20141014.bed.gz +C0011I43.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_50_55_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C0011I43.DNase.hotspot_v3.20130415.bed.gz +S00EPZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS/S00EPZ41.DNase.hotspot_v3.20141014.bed.gz +C001UY46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C001UY46.DNase.hotspot_v3.20130415.bed.gz +S00HRJ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00HRJ41.DNase.hotspot_v3.20141014.bed.gz +C004084E.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C004084E.DNase.hotspot_v3.20130415.bed.gz +S00HSH41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00HSH41.DNase.hotspot_v3.20141014.bed.gz +C005PS4E.DNase.hotspot_v3.20130819.bed NCMLS DHS CD14_positive_CD16_negative_classical_monocyte Cord Blood CD14_positive_CD16_negative_classical_monocyte Female NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C005PS4E.DNase.hotspot_v3.20130819.bed.gz +S00HTF41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00HTF41.DNase.hotspot_v3.20141014.bed.gz +C005VG45.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS/C005VG45.DNase.hotspot_v3.20130819.bed.gz +S00JPF41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS/S00JPF41.DNase.hotspot_v3.20141014.bed.gz +C006NS47.DNase.hotspot_v3.20130819.bed NCMLS DHS CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Cord Blood CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Male NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS/C006NS47.DNase.hotspot_v3.20130819.bed.gz +S00JQD41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00JQD41.DNase.hotspot_v3.20141014.bed.gz +C006UE47.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_65_70_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS/C006UE47.DNase.hotspot_v3.20130819.bed.gz +S00JRB41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00JRB41.DNase.hotspot_v3.20141014.bed.gz +S001MJ48.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS/S001MJ48.DNase.hotspot_v3.20130819.bed.gz +S00JS941.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00JS941.DNase.hotspot_v3.20141014.bed.gz +S001MJ4A.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS/S001MJ4A.DNase.hotspot_v3.20130819.bed.gz +bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line KARPAS-422_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS/bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed.gz +S005FH41.DNase.hotspot_v3.20130819.bed NCMLS DHS Acute_myeloid_leukemia Bone Marrow Acute_myeloid_leukemia Female_70_75_years_Acute_Myeloid_leukaemia NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS/S005FH41.DNase.hotspot_v3.20130819.bed.gz +bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line SU-DHL-5_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS/bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed.gz +S00BXV41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00BXV41.DNase.hotspot_v3.20141014.bed.gz +S00BYT41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00BYT41.DNase.hotspot_v3.20141014.bed.gz diff --git a/database/encode.decode b/database/encode.decode new file mode 100644 index 0000000..3e67025 --- /dev/null +++ b/database/encode.decode @@ -0,0 +1,126 @@ +file lab datatype cell tissue shortcell individual acc url +A549-all.twopass.merge150.wgt10.zgt2.wig Combined DHS A549 Epithelium A549 NA "GSM816649,GSM736580,GSM736506" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/A549-all.twopass.merge150.wgt10.zgt2.wig +Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Adult_CD4+ Blood Adult_CD4+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig UW DHS AG04449 Skin AG04449 NA "GSM736562,GSM736590" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig +AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig UW DHS AG04450 Lung AG04450 NA "GSM736514,GSM736563" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig +AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig UW DHS AG09309 Skin AG09309 NA "GSM736551,GSM736616" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig +AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig UW DHS AG09319 Gingival AG09319 NA "GSM736531,GSM736619" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig +AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig UW DHS AG10803 Skin AG10803 NA "GSM736598,GSM736633" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig +AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig UW DHS AoAF Blood vessel AoAF NA "GSM736583,GSM736505" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig +BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig UW DHS BE2_C Brain BE2_C NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig +BJ-DS10081.twopass.merge150.wgt10.zgt2.wig UW DHS BJ Skin BJ NA "GSM736518,GSM736596" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BJ-DS10081.twopass.merge150.wgt10.zgt2.wig +CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig UW DHS Caco-2 Colon Caco-2 NA "GSM736500,GSM736587" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig +CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD14+ Blood CD14+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig +CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD20+ Blood CD20+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig +CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD34+ Blood CD34+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig +CMK-DS12393.twopass.merge150.wgt10.zgt2.wig UW DHS CMK Blood CMK NA GSM736607 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CMK-DS12393.twopass.merge150.wgt10.zgt2.wig +E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS E_myoblast Muscle E_myoblast NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig UW DHS GM06990 Blood GM06990 NA "GSM736558,GSM736635" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig +GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig UW DHS GM12864 Blood GM12864 NA GSM736525 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig +GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig UW DHS GM12865 Blood GM12865 NA "GSM736512,GSM736561" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig +GM12878-all.twopass.merge150.wgt10.zgt2.wig Combined DHS GM12878 Blood GM12878 NA "GSM816665,GSM736496,GSM736620" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12878-all.twopass.merge150.wgt10.zgt2.wig +HAc-DS14765.twopass.merge150.wgt10.zgt2.wig UW DHS HAc Cerebellar HAc NA "GSM736586,GSM736538" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAc-DS14765.twopass.merge150.wgt10.zgt2.wig +HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig UW DHS HAEpiC Epithelium HAEpiC NA "GSM736631,GSM736606" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig +HAh-DS15192.twopass.merge150.wgt10.zgt2.wig UW DHS HA-h Brain hippocampus HA-h NA "GSM736594,GSM736535" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAh-DS15192.twopass.merge150.wgt10.zgt2.wig +HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig UW DHS HA-sp Spinal cord HA-sp NA "GSM736537,GSM736625" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig +HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig UW DHS HBMEC Blood vessel HBMEC NA "GSM736509,GSM736554" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig +HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig UW DHS HCFaa Heart HCFaa NA "GSM736494,GSM736601" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig +HCF-DS12501.twopass.merge150.wgt10.zgt2.wig UW DHS HCF Heart HCF NA "GSM736568,GSM736540" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCF-DS12501.twopass.merge150.wgt10.zgt2.wig +HCM-DS12599.twopass.merge150.wgt10.zgt2.wig UW DHS HCM Heart HCM NA "GSM736516,GSM736504" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCM-DS12599.twopass.merge150.wgt10.zgt2.wig +HConF-DS11642.twopass.merge150.wgt10.zgt2.wig UW DHS HConF Eye HConF NA "GSM736547,GSM736515" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HConF-DS11642.twopass.merge150.wgt10.zgt2.wig +HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig UW DHS HCPEpiC Epithelium HCPEpiC NA "GSM736569,GSM736597" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig +HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig UW DHS HCT-116 Colon HCT-116 NA "GSM736600,GSM736493" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig +HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig UW DHS HEEpiC Epithelium HEEpiC NA "GSM736585,GSM736532" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig +Hela-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Hela-all.twopass.merge150.wgt10.zgt2.wig +HepG2-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HepG2 Liver HepG2 NA "GSM816662,GSM736637,GSM736639" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HepG2-all.twopass.merge150.wgt10.zgt2.wig +HESC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HESC ES Cell HESC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HESC-all.twopass.merge150.wgt10.zgt2.wig +hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig UW DHS hESCT0 ES Cell hESCT0 NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig +HFF-DS15115.twopass.merge150.wgt10.zgt2.wig UW DHS HFF Foreskin HFF NA "GSM736602,GSM736572" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF-DS15115.twopass.merge150.wgt10.zgt2.wig +HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig UW DHS HFF-Myc Foreskin HFF-Myc NA "GSM736524,GSM736605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig +HGF-DS11752.twopass.merge150.wgt10.zgt2.wig UW DHS HGF Gingival HGF NA "GSM736579,GSM736576" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HGF-DS11752.twopass.merge150.wgt10.zgt2.wig +HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig UW DHS HIPEpiC Epithelium HIPEpiC NA "GSM736589,GSM736615" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig +HL60-DS11809.twopass.merge150.wgt10.zgt2.wig UW DHS HL-60 Blood HL-60 NA "GSM736626,GSM736595" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HL60-DS11809.twopass.merge150.wgt10.zgt2.wig +HMEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HMEC Breast HMEC NA "GSM816669,GSM736634,GSM736552" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMEC-all.twopass.merge150.wgt10.zgt2.wig +HMF-DS13363.twopass.merge150.wgt10.zgt2.wig UW DHS HMF Breast HMF NA "GSM736628,GSM736541" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMF-DS13363.twopass.merge150.wgt10.zgt2.wig +HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dAd Blood vessel HMVEC-dAd NA "GSM1024745,GSM1024747" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig +HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Ad Blood vessel HMVEC-dBl-Ad NA "GSM736609,GSM736523" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig +HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Neo Blood vessel HMVEC-dBl-Neo NA "GSM736571,GSM736521" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig +HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Ad Blood vessel HMVEC-dLy-Ad NA "GSM736599,GSM736591" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig +HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Neo Blood vessel HMVEC-dLy-Neo NA "GSM736577,GSM736573" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig +HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dNeo Blood vessel HMVEC-dNeo NA "GSM736611,GSM736624" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig +HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LBl Blood vessel HMVEC-LBl NA "GSM736542,GSM736511" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig +HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LLy Blood vessel HMVEC-LLy NA "GSM736507,GSM736627" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig +HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig UW DHS HNPCEpiC Epithelium HNPCEpiC NA "GSM736621,GSM736550" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig +HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HPAEC Blood vessel HPAEC NA GSM1024763 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig +HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig UW DHS HPAF Blood vessel HPAF NA "GSM736555,GSM736614" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig +HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig UW DHS HPdLF Epithelium HPdLF NA "GSM736632,GSM736528" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig +HPF-DS13390.twopass.merge150.wgt10.zgt2.wig UW DHS HPF Lung HPF NA "GSM736574,GSM736503" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPF-DS13390.twopass.merge150.wgt10.zgt2.wig +HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig UW DHS HRCEpiC Epithelium HRCEpiC NA "GSM736549,GSM736557" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig +HRE-DS10641.twopass.merge150.wgt10.zgt2.wig UW DHS HRE Epithelium HRE NA "GSM736527,GSM736548" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRE-DS10641.twopass.merge150.wgt10.zgt2.wig +HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig UW DHS HRGEC Kidney HRGEC NA "GSM736499,GSM736618" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig +HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig UW DHS HRPEpiC Epithelium HRPEpiC NA "GSM736630,GSM736623" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig +HSMM-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM-all.twopass.merge150.wgt10.zgt2.wig +HSMM_D-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM_D-all.twopass.merge150.wgt10.zgt2.wig +hTH1-all.twopass.merge150.wgt10.zgt2.wig Combined DHS Th1 Blood Th1 NA "GSM736592,GSM1024760" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH1-all.twopass.merge150.wgt10.zgt2.wig +hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig UW DHS Th2 Blood Th2 NA "GSM736502,GSM1024792" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig +HUVEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HUVEC Blood vessel HUVEC NA "GSM816646,GSM736575,GSM736533" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HUVEC-all.twopass.merge150.wgt10.zgt2.wig +HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig UW DHS HVMF Connective HVMF NA "GSM736534,GSM736491" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig +Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig UW DHS Jurkat Blood Jurkat NA "GSM736501,GSM736492" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig +K562-all.twopass.merge150.wgt10.zgt2.wig Combined DHS K562 Blood K562 NA "GSM816655,GSM1008602,GSM1008567,GSM1008601,GSM1008558,GSM1008580,GSM736629,GSM736566" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/K562-all.twopass.merge150.wgt10.zgt2.wig +LNCap-all.twopass.merge150.wgt10.zgt2.wig Combined DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/LNCap-all.twopass.merge150.wgt10.zgt2.wig +MCF7-all.twopass.merge150.wgt10.zgt2.wig Combined DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/MCF7-all.twopass.merge150.wgt10.zgt2.wig +NB4-DS12543.twopass.merge150.wgt10.zgt2.wig UW DHS NB4 Blood NB4 NA "GSM736604,GSM736529" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NB4-DS12543.twopass.merge150.wgt10.zgt2.wig +NHA-DS12800.twopass.merge150.wgt10.zgt2.wig UW DHS NH-A Nervous NH-A NA "GSM736544,GSM736584" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHA-DS12800.twopass.merge150.wgt10.zgt2.wig +NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-Ad Skin NHDF-Ad NA "GSM736567,GSM736520" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig +NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-neo Skin NHDF-neo NA "GSM736498,GSM736546" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig +NHEK-all.twopass.merge150.wgt10.zgt2.wig Combined DHS NHEK Skin NHEK NA "GSM816635,GSM736545,GSM736556" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHEK-all.twopass.merge150.wgt10.zgt2.wig +NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig UW DHS NHLF Lung NHLF NA "GSM736612,GSM736536" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig +NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS NT2-D1 Testis NT2-D1 NA "GSM1024751,GSM1024795" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig +PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig UW DHS PANC-1 Pancreas PANC-1 NA "GSM736517,GSM736519" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig +PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS PrEC Prostate PrEC NA "GSM1024742,GSM1024743" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig +RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig UW DHS RPTEC Epithelium RPTEC NA "GSM736543,GSM736539" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig +RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS RWPE1 Prostate RWPE1 NA GSM1008595 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig UW DHS SAEC Epithelium SAEC NA "GSM736608,GSM736617" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig +SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig UW DHS SKMC Muscle SKMC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig +SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-MC Brain SK-N-MC NA "GSM736522,GSM736570" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig +SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-SH Brain SK-N-SH NA GSM1008585 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig +WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig UW DHS WERI-Rb-1 Eye WERI-Rb-1 NA "GSM736495,GSM736636" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS 8988T Liver 8988T NA GSM816667 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS AoSMC Blood vessel AoSMC NA GSM816638 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Chorion Fetal membrane Chorion NA GSM816628 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS CLL Blood CLL NA GSM816664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Fibrobl Skin Fibrobl NA GSM816652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS FibroP Skin FibroP NA GSM816626 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Gliobla Brain Gliobla NA GSM816668 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12891 Blood GM12891 NA GSM816656 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12892 Blood GM12892 NA GSM816657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM18507 Blood GM18507 NA GSM816653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19238 Blood GM19238 NA GSM816658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19239 Blood GM19239 NA GSM816659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19240 Blood GM19240 NA GSM816648 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS H9ES ES Cell H9ES NA GSM816629 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Hepatocytes Liver Hepatocytes NA GSM816663 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HPDE6-E6E7 Pancreatic duct HPDE6-E6E7 NA GSM816639 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HTR8svn Blastula HTR8svn NA GSM816644 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7.5 Liver Huh-7.5 NA GSM816671 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7 Liver Huh-7 NA GSM816641 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS iPS IPS iPS NA GSM816642 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Medullo Brain Medullo NA GSM816636 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Melano Skin Melano NA GSM816631 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Myometr Myometrium Myometr NA GSM816630 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Osteobl Bone Osteobl NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIsletD Pancreas PanIsletD NA GSM816666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIslets Pancreas PanIslets NA GSM816660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS pHTE Epithelium pHTE NA GSM816647 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS ProgFib Skin ProgFib NA GSM816661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Stellate Liver Stellate NA GSM816672 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS T-47D Breast T-47D NA "GSM816673,GSM1008576,GSM1024762,GSM1024761" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig +WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig \ No newline at end of file diff --git a/database/erc.decode b/database/erc.decode new file mode 100644 index 0000000..bd80775 --- /dev/null +++ b/database/erc.decode @@ -0,0 +1,300 @@ +file lab datatype cell tissue shortcell individual acc url +UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Breast_vHMEC.RM035 Breast Breast_vHMEC RM035 GSM753973 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.twopass.merge150.wgt10.zgt2.wig.gz +UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18438.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Breast_vHMEC.RM035 Breast Breast_vHMEC RM035 GSM753974 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18438.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01689.DS17391.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD14_Primary_Cells.RO_01689+ Blood CD14 RO_01689+ GSM701503 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01689.DS17391.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01701.DS17889.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD14_Primary_Cells.RO_01701+ Blood CD14 RO_01701+ GSM701541 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01701.DS17889.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01679.DS17186.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01679+ Blood CD19 RO_01679+ GSM701492 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01679.DS17186.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01689.DS17281.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01689+ Blood CD19 RO_01689+ GSM701493 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01689.DS17281.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01701.DS17440.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01701+ Blood CD19 RO_01701+ GSM701507 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01701.DS17440.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD20_Primary_Cells.ChromatinAccessibility.RO_01778.DS17371.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD20_Primary_Cells.RO_01778+ Blood CD20 RO_01778+ GSM701500 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD20_Primary_Cells.ChromatinAccessibility.RO_01778.DS17371.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD3_Primary_Cells.ChromatinAccessibility.CB1_1-3-2011.DS17702.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.CB1_1-3-2011+ Blood CD3 CB1_1-3-2011+ GSM701525 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.CB1_1-3-2011.DS17702.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.CB6_1-4-2011+ Blood CD3 CB6_1-4-2011+ GSM701526 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS17198.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.RO_01679+ Blood CD3 RO_01679+ GSM665837 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS17198.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01701.DS17534.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.RO_01701+ Blood CD3 RO_01701+ GSM701516 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01701.DS17534.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01549.DS15947.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD4_Primary_Cells.RO_01549+ Blood CD4 RO_01549+ GSM665812 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01549.DS15947.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD4_Primary_Cells.RO_01679+ Blood CD4 RO_01679+ GSM665839 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01689.DS17329.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD4_Primary_Cells.RO_01689+ Blood CD4 RO_01689+ GSM817166 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01689.DS17329.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17881.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD4_Primary_Cells.RO_01701+ Blood CD4 RO_01701+ GSM701539 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17881.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01679.DS17189.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD56_Primary_Cells.RO_01679+ Blood CD56 RO_01679+ GSM665836 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01679.DS17189.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01701.DS17443.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD56_Primary_Cells.RO_01701+ Blood CD56 RO_01701+ GSM701508 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01701.DS17443.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01549.DS16012.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD8_Primary_Cells.RO_01549+ Blood CD8 RO_01549+ GSM665813 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01549.DS16012.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD8_Primary_Cells.RO_01679+ Blood CD8 RO_01679+ GSM665838 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01689.DS17332.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD8_Primary_Cells.RO_01689+ Blood CD8 RO_01689+ GSM701499 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01689.DS17332.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01701.DS17885.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD8_Primary_Cells.RO_01701+ Blood CD8 RO_01701+ GSM701540 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01701.DS17885.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-22662.DS12528.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Adrenal_Gland.H-22662 Fetal Adrenal Fetal_Adrenal_Gland H-22662 GSM530653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-22662.DS12528.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-23769.DS17319.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Adrenal_Gland.H-23769 Fetal Adrenal Fetal_Adrenal_Gland H-23769 GSM817165 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-23769.DS17319.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24409.DS20343.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Adrenal_Gland.H-24409 Fetal Adrenal Fetal_Adrenal_Gland H-24409 GSM878658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24409.DS20343.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11872.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-22510 Fetal Brain Fetal_Brain H-22510 GSM530651 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11872.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11877.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-22510 Fetal Brain Fetal_Brain H-22510 GSM595913 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11877.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-22911.DS14464.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-22911 Fetal Brain Fetal_Brain H-22911 GSM595920 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-22911.DS14464.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14717.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23266 Fetal Brain Fetal_Brain H-23266 GSM595922 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14717.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23266 Fetal Brain Fetal_Brain H-23266 GSM595923 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14803.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23284 Fetal Brain Fetal_Brain H-23284 GSM595926 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14803.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14815.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23284 Fetal Brain Fetal_Brain H-23284 GSM595928 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14815.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23399 Fetal Brain Fetal_Brain H-23399 GSM665804 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23548.DS16302.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23548 Fetal Brain Fetal_Brain H-23548 GSM665819 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23548.DS16302.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-24279.DS20221.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-24279 Fetal Brain Fetal_Brain H-24279 GSM878650 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-24279.DS20221.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-24297.DS20226.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-24297 Fetal Brain Fetal_Brain H-24297 GSM878651 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-24297.DS20226.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-24381.DS20231.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-24381 Fetal Brain Fetal_Brain H-24381 GSM878652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-24381.DS20231.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-22662 Fetal Heart Fetal_Heart H-22662 GSM530654 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-22727.DS12810.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-22727 Fetal Heart Fetal_Heart H-22727 GSM530661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-22727.DS12810.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23468.DS15839.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23468 Fetal Heart Fetal_Heart H-23468 GSM665811 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23468.DS15839.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23500.DS16018.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23500 Fetal Heart Fetal_Heart H-23500 GSM665814 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23500.DS16018.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23524.DS16146.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23524 Fetal Heart Fetal_Heart H-23524 GSM665817 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23524.DS16146.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23589 Fetal Heart Fetal_Heart H-23589 GSM665824 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23604.DS16582.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23604 Fetal Heart Fetal_Heart H-23604 GSM665830 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23604.DS16582.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23617.DS16621.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23617 Fetal Heart Fetal_Heart H-23617 GSM665831 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23617.DS16621.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23663.DS16819.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23663 Fetal Heart Fetal_Heart H-23663 GSM774203 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23663.DS16819.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23744.DS19431.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23744 Fetal Heart Fetal_Heart H-23744 GSM817220 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23744.DS19431.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-24042.DS19427.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-24042 Fetal Heart Fetal_Heart H-24042 GSM878630 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-24042.DS19427.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23500.DS16027.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23500 "Fetal Intestine, Large" Fetal_Intestine_Large H-23500 GSM665815 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23500.DS16027.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23524.DS16164.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23524 "Fetal Intestine, Large" Fetal_Intestine_Large H-23524 GSM665818 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23524.DS16164.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23604.DS16563.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23604 "Fetal Intestine, Large" Fetal_Intestine_Large H-23604 GSM665826 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23604.DS16563.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23744.DS17094.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23744 "Fetal Intestine, Large" Fetal_Intestine_Large H-23744 GSM817162 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23744.DS17094.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23758.DS17157.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23758 "Fetal Intestine, Large" Fetal_Intestine_Large H-23758 GSM701490 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23758.DS17157.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23769 "Fetal Intestine, Large" Fetal_Intestine_Large H-23769 GSM701495 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23808.DS17422.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23808 "Fetal Intestine, Large" Fetal_Intestine_Large H-23808 GSM774213 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23808.DS17422.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23833.DS17462.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23833 "Fetal Intestine, Large" Fetal_Intestine_Large H-23833 GSM774214 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23833.DS17462.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23855.DS17502.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23855 "Fetal Intestine, Large" Fetal_Intestine_Large H-23855 GSM701514 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23855.DS17502.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23887.DS17647.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23887 "Fetal Intestine, Large" Fetal_Intestine_Large H-23887 GSM774217 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23887.DS17647.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23914.DS17748.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23914 "Fetal Intestine, Large" Fetal_Intestine_Large H-23914 GSM774220 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23914.DS17748.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23941.DS17785.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23941 "Fetal Intestine, Large" Fetal_Intestine_Large H-23941 GSM701531 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23941.DS17785.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23964.DS17841.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23964 "Fetal Intestine, Large" Fetal_Intestine_Large H-23964 GSM774228 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23964.DS17841.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24005.DS17990.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-24005 "Fetal Intestine, Large" Fetal_Intestine_Large H-24005 GSM774233 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24005.DS17990.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24111.DS18499.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-24111 "Fetal Intestine, Large" Fetal_Intestine_Large H-24111 GSM817188 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24111.DS18499.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23604.DS16559.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23604 "Fetal Intestine, Small" Fetal_Intestine_Small H-23604 GSM665825 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23604.DS16559.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23640.DS16712.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23640 "Fetal Intestine, Small" Fetal_Intestine_Small H-23640 GSM701487 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23640.DS16712.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23663.DS16822.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23663 "Fetal Intestine, Small" Fetal_Intestine_Small H-23663 GSM665835 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23663.DS16822.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23724.DS16975.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23724 "Fetal Intestine, Small" Fetal_Intestine_Small H-23724 GSM817161 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23724.DS16975.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23744.DS17092.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23744 "Fetal Intestine, Small" Fetal_Intestine_Small H-23744 GSM774205 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23744.DS17092.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23758.DS17150.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23758 "Fetal Intestine, Small" Fetal_Intestine_Small H-23758 GSM774210 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23758.DS17150.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23769.DS17317.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23769 "Fetal Intestine, Small" Fetal_Intestine_Small H-23769 GSM701496 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23769.DS17317.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23808.DS17425.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23808 "Fetal Intestine, Small" Fetal_Intestine_Small H-23808 GSM701504 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23808.DS17425.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23864.DS17844.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23864 "Fetal Intestine, Small" Fetal_Intestine_Small H-23864 GSM774229 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23864.DS17844.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23887.DS17643.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23887 "Fetal Intestine, Small" Fetal_Intestine_Small H-23887 GSM774216 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23887.DS17643.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23914.DS17763.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23914 "Fetal Intestine, Small" Fetal_Intestine_Small H-23914 GSM701530 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23914.DS17763.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23941.DS17808.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23941 "Fetal Intestine, Small" Fetal_Intestine_Small H-23941 GSM774225 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23941.DS17808.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-24111.DS18495.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-24111 "Fetal Intestine, Small" Fetal_Intestine_Small H-24111 GSM817187 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-24111.DS18495.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-22337 Fetal Kidney Fetal_Kidney H-22337 GSM493385 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-22676.DS12635.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-22676 Fetal Kidney Fetal_Kidney H-22676 GSM530655 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-22676.DS12635.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-23524.DS16139.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-23524 Fetal Kidney Fetal_Kidney H-23524 GSM665816 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-23524.DS16139.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-23663.DS16837.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-23663 Fetal Kidney Fetal_Kidney H-23663 GSM817159 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-23663.DS16837.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-23855.DS17522.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-23855 Fetal Kidney Fetal_Kidney H-23855 GSM701515 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-23855.DS17522.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-23914.DS17753.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-23914 Fetal Kidney Fetal_Kidney H-23914 GSM774221 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-23914.DS17753.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-24507.DS20564.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-24507 Fetal Kidney Fetal_Kidney H-24507 GSM878666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-24507.DS20564.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23589.DS16446.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Left.H-23589 Fetal Kidney Fetal_Kidney_Left H-23589 GSM665822 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23589.DS16446.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23604.DS16579.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Left.H-23604 Fetal Kidney Fetal_Kidney_Left H-23604 GSM665829 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23604.DS16579.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23640.DS16805.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Left.H-23640 Fetal Kidney Fetal_Kidney_Left H-23640 GSM665834 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23640.DS16805.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Left.H-23758 Fetal Kidney Fetal_Kidney_Left H-23758 GSM774209 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24089.DS18466.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Left.H-24089 Fetal Kidney Fetal_Kidney_Left H-24089 GSM817181 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24089.DS18466.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23435.DS15651.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Right.H-23435 Fetal Kidney Fetal_Kidney_Right H-23435 GSM665810 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23435.DS15651.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23589.DS16441.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Right.H-23589 Fetal Kidney Fetal_Kidney_Right H-23589 GSM665821 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23589.DS16441.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23640.DS16801.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Right.H-23640 Fetal Kidney Fetal_Kidney_Right H-23640 GSM665833 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23640.DS16801.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23758.DS17144.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Right.H-23758 Fetal Kidney Fetal_Kidney_Right H-23758 GSM817163 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23758.DS17144.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24089.DS18463.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Right.H-24089 Fetal Kidney Fetal_Kidney_Right H-24089 GSM817180 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24089.DS18463.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-22676.DS12646.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-22676 Fetal Lung Fetal_Lung H-22676 GSM530656 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-22676.DS12646.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-22727.DS12817.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-22727 Fetal Lung Fetal_Lung H-22727 GSM530662 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-22727.DS12817.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-22934B.DS13507.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-22934B Fetal Lung Fetal_Lung H-22934B GSM595915 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-22934B.DS13507.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23090.DS13985.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23090 Fetal Lung Fetal_Lung H-23090 GSM595916 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23090.DS13985.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23247.DS14666.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23247 Fetal Lung Fetal_Lung H-23247 GSM595921 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23247.DS14666.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23266.DS14724.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23266 Fetal Lung Fetal_Lung H-23266 GSM595924 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23266.DS14724.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23266.DS14751.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23266 Fetal Lung Fetal_Lung H-23266 GSM595925 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23266.DS14751.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23284.DS14809.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23284 Fetal Lung Fetal_Lung H-23284 GSM595927 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23284.DS14809.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23284.DS14820.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23284 Fetal Lung Fetal_Lung H-23284 GSM595929 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23284.DS14820.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23365.DS15227.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23365 Fetal Lung Fetal_Lung H-23365 GSM595930 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23365.DS15227.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23399.DS15461.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23399 Fetal Lung Fetal_Lung H-23399 GSM665805 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23399.DS15461.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung.ChromatinAccessibility.H-23419.DS15573.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung.H-23419 Fetal Lung Fetal_Lung H-23419 GSM665806 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung.ChromatinAccessibility.H-23419.DS15573.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23435.DS15637.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23435 Fetal Lung Fetal_Lung_Left H-23435 GSM665808 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23435.DS15637.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23604.DS16570.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23604 Fetal Lung Fetal_Lung_Left H-23604 GSM665828 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23604.DS16570.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23640.DS18170.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23640 Fetal Lung Fetal_Lung_Left H-23640 GSM774237 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23640.DS18170.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23744.DS17105.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23744 Fetal Lung Fetal_Lung_Left H-23744 GSM774207 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23744.DS17105.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23758.DS17154.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23758 Fetal Lung Fetal_Lung_Left H-23758 GSM774211 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23758.DS17154.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23833.DS17464.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23833 Fetal Lung Fetal_Lung_Left H-23833 GSM701512 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23833.DS17464.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23887.DS17674.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23887 Fetal Lung Fetal_Lung_Left H-23887 GSM701524 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23887.DS17674.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23914.DS17739.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23914 Fetal Lung Fetal_Lung_Left H-23914 GSM701527 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23914.DS17739.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-23964.DS17835.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-23964 Fetal Lung Fetal_Lung_Left H-23964 GSM701534 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-23964.DS17835.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-24005.DS17959.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-24005 Fetal Lung Fetal_Lung_Left H-24005 GSM817168 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-24005.DS17959.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-24089.DS18421.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-24089 Fetal Lung Fetal_Lung_Left H-24089 GSM817175 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-24089.DS18421.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Left.ChromatinAccessibility.H-24111.DS18487.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Left.H-24111 Fetal Lung Fetal_Lung_Left H-24111 GSM817185 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Left.ChromatinAccessibility.H-24111.DS18487.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23435.DS15632.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23435 Fetal Lung Fetal_Lung_Right H-23435 GSM665807 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23435.DS15632.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23604.DS16566.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23604 Fetal Lung Fetal_Lung_Right H-23604 GSM665827 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23604.DS16566.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23640.DS16790.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23640 Fetal Lung Fetal_Lung_Right H-23640 GSM665832 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23640.DS16790.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23744.DS17101.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23744 Fetal Lung Fetal_Lung_Right H-23744 GSM774206 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23744.DS17101.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23758.DS17162.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23758 Fetal Lung Fetal_Lung_Right H-23758 GSM817164 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23758.DS17162.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23887.DS17670.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23887 Fetal Lung Fetal_Lung_Right H-23887 GSM701523 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23887.DS17670.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23964.DS17831.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23964 Fetal Lung Fetal_Lung_Right H-23964 GSM774227 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23964.DS17831.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-24005.DS17954.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-24005 Fetal Lung Fetal_Lung_Right H-24005 GSM774231 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-24005.DS17954.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-24089.DS18418.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-24089 Fetal Lung Fetal_Lung_Right H-24089 GSM817174 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-24089.DS18418.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-24111.DS18492.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-24111 Fetal Lung Fetal_Lung_Right H-24111 GSM817186 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-24111.DS18492.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23808.DS17432.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-23808 Fetal Muscle Fetal_Muscle_Arm H-23808 GSM701506 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23808.DS17432.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23914.DS17765.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-23914 Fetal Muscle Fetal_Muscle_Arm H-23914 GSM774223 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23914.DS17765.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23941.DS17825.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-23941 Fetal Muscle Fetal_Muscle_Arm H-23941 GSM774226 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23941.DS17825.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23964.DS17848.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-23964 Fetal Muscle Fetal_Muscle_Arm H-23964 GSM701535 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23964.DS17848.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24005.DS18080.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24005 Fetal Muscle Fetal_Muscle_Arm H-24005 GSM774234 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24005.DS18080.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24042.DS18176.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24042 Fetal Muscle Fetal_Muscle_Arm H-24042 GSM774239 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24042.DS18176.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24078.DS18379.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24078 Fetal Muscle Fetal_Muscle_Arm H-24078 GSM878610 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24078.DS18379.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24089.DS18452.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24089 Fetal Muscle Fetal_Muscle_Arm H-24089 GSM817178 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24089.DS18452.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24111.DS18473.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24111 Fetal Muscle Fetal_Muscle_Arm H-24111 GSM817184 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24111.DS18473.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24125.DS18559.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24125 Fetal Muscle Fetal_Muscle_Arm H-24125 GSM817191 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24125.DS18559.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24143.DS18992.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24143 Fetal Muscle Fetal_Muscle_Arm H-24143 GSM878618 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24143.DS18992.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24198.DS19051.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24198 Fetal Muscle Fetal_Muscle_Arm H-24198 GSM878619 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24198.DS19051.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24218.DS19053.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24218 Fetal Muscle Fetal_Muscle_Arm H-24218 GSM878620 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24218.DS19053.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24244 Fetal Muscle Fetal_Muscle_Arm H-24244 GSM878625 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24259.DS19295.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24259 Fetal Muscle Fetal_Muscle_Arm H-24259 GSM817214 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24259.DS19295.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24272.DS19380.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24272 Fetal Muscle Fetal_Muscle_Arm H-24272 GSM817216 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24272.DS19380.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24297.DS19646.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24297 Fetal Muscle Fetal_Muscle_Arm H-24297 GSM878638 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24297.DS19646.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23914.DS17767.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-23914 Fetal Muscle Fetal_Muscle_Back H-23914 GSM774224 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23914.DS17767.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23964.DS17850.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-23964 Fetal Muscle Fetal_Muscle_Back H-23964 GSM701536 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23964.DS17850.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24005.DS18083.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24005 Fetal Muscle Fetal_Muscle_Back H-24005 GSM774235 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24005.DS18083.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24078.DS18377.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24078 Fetal Muscle Fetal_Muscle_Back H-24078 GSM817171 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24078.DS18377.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24089.DS18454.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24089 Fetal Muscle Fetal_Muscle_Back H-24089 GSM878611 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24089.DS18454.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24111.DS18468.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24111 Fetal Muscle Fetal_Muscle_Back H-24111 GSM817182 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24111.DS18468.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24143.DS18842.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24143 Fetal Muscle Fetal_Muscle_Back H-24143 GSM817200 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24143.DS18842.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24218.DS19117.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24218 Fetal Muscle Fetal_Muscle_Back H-24218 GSM817207 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24218.DS19117.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24244.DS19283.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24244 Fetal Muscle Fetal_Muscle_Back H-24244 GSM817212 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24244.DS19283.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24272.DS19384.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24272 Fetal Muscle Fetal_Muscle_Back H-24272 GSM817217 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24272.DS19384.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24279.DS19441.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24279 Fetal Muscle Fetal_Muscle_Back H-24279 GSM878632 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24279.DS19441.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24297.DS19648.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24297 Fetal Muscle Fetal_Muscle_Back H-24297 GSM878639 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24297.DS19648.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24409.DS20244.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24409 Fetal Muscle Fetal_Muscle_Back H-24409 GSM878655 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24409.DS20244.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-23808.DS17429.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-23808 Fetal Muscle Fetal_Muscle_Leg H-23808 GSM701505 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-23808.DS17429.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24078.DS18386.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24078 Fetal Muscle Fetal_Muscle_Leg H-24078 GSM774242 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24078.DS18386.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24089.DS18456.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24089 Fetal Muscle Fetal_Muscle_Leg H-24089 GSM817179 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24089.DS18456.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24111.DS18471.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24111 Fetal Muscle Fetal_Muscle_Leg H-24111 GSM817183 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24111.DS18471.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24143.DS18844.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24143 Fetal Muscle Fetal_Muscle_Leg H-24143 GSM817201 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24143.DS18844.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24198.DS19158.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24198 Fetal Muscle Fetal_Muscle_Leg H-24198 GSM878622 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24198.DS19158.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24218.DS19115.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24218 Fetal Muscle Fetal_Muscle_Leg H-24218 GSM817206 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24218.DS19115.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24244.DS19272.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24244 Fetal Muscle Fetal_Muscle_Leg H-24244 GSM878626 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24244.DS19272.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24259.DS19291.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24259 Fetal Muscle Fetal_Muscle_Leg H-24259 GSM817213 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24259.DS19291.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24279.DS19436.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24279 Fetal Muscle Fetal_Muscle_Leg H-24279 GSM878631 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24279.DS19436.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24297.DS19643.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24297 Fetal Muscle Fetal_Muscle_Leg H-24297 GSM878637 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24297.DS19643.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24409.DS20239.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24409 Fetal Muscle Fetal_Muscle_Leg H-24409 GSM878653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24409.DS20239.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Lower_Limb_Skeletal.ChromatinAccessibility.H-24042.DS18174.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Lower_Limb_Skeletal.H-24042 Fetal Muscle Fetal_Muscle_Lower_Limb_Skeletal H-24042 GSM774238 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Lower_Limb_Skeletal.ChromatinAccessibility.H-24042.DS18174.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-23941.DS17827.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Trunk.H-23941 Fetal Muscle Fetal_Muscle_Trunk H-23941 GSM701533 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-23941.DS17827.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24409.DS20242.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Trunk.H-24409 Fetal Muscle Fetal_Muscle_Trunk H-24409 GSM878654 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24409.DS20242.twopass.merge150.wgt10.zgt2.wig.gz 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ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Upper_Trunk.ChromatinAccessibility.H-23887.DS17664.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Placenta.ChromatinAccessibility.H-23887.DS17639.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Placenta.H-23887 Fetal Placenta Fetal_Placenta H-23887 GSM774215 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Placenta.ChromatinAccessibility.H-23887.DS17639.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Placenta.ChromatinAccessibility.H-23914.DS17744.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Placenta.H-23914 Fetal Placenta Fetal_Placenta H-23914 GSM774219 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Placenta.ChromatinAccessibility.H-23914.DS17744.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Placenta.ChromatinAccessibility.H-24272.DS19391.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Placenta.H-24272 Fetal Placenta Fetal_Placenta H-24272 GSM817219 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Placenta.ChromatinAccessibility.H-24272.DS19391.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Placenta.ChromatinAccessibility.H-24409.DS20346.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Placenta.H-24409 Fetal Placenta Fetal_Placenta H-24409 GSM878659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Placenta.ChromatinAccessibility.H-24409.DS20346.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23769.DS17307.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23769 Fetal Renal Cortex Fetal_Renal_Cortex H-23769 GSM701494 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23769.DS17307.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23790.DS17387.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23790 Fetal Renal Cortex Fetal_Renal_Cortex H-23790 GSM701502 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23790.DS17387.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23833.DS17455.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23833 Fetal Renal Cortex Fetal_Renal_Cortex H-23833 GSM701511 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23833.DS17455.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23914.DS17756.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23914 Fetal Renal Cortex Fetal_Renal_Cortex H-23914 GSM701529 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23914.DS17756.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23941.DS17804.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23941 Fetal Renal Cortex Fetal_Renal_Cortex H-23941 GSM701532 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23941.DS17804.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24078.DS18428.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-24078 Fetal Renal Cortex Fetal_Renal_Cortex H-24078 GSM817176 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24078.DS18428.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24259.DS19388.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-24259 Fetal Renal Cortex Fetal_Renal_Cortex H-24259 GSM878629 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24259.DS19388.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24493.DS20568.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-24493 Fetal Renal Cortex Fetal_Renal_Cortex H-24493 GSM878667 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24493.DS20568.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-23871.DS17550.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Left.H-23871 Fetal Renal Cortex Fetal_Renal_Cortex_Left H-23871 GSM701519 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-23871.DS17550.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24111.DS18542.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Left.H-24111 Fetal Renal Cortex Fetal_Renal_Cortex_Left H-24111 GSM817190 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24111.DS18542.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Left.H-24169 Fetal Renal Cortex Fetal_Renal_Cortex_Left H-24169 GSM817203 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24232.DS19257.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Left.H-24232 Fetal Renal Cortex Fetal_Renal_Cortex_Left H-24232 GSM817211 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24232.DS19257.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-23871.DS17545.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Right.H-23871 Fetal Renal Cortex Fetal_Renal_Cortex_Right H-23871 GSM701517 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-23871.DS17545.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24169.DS18928.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Right.H-24169 Fetal Renal Cortex Fetal_Renal_Cortex_Right H-24169 GSM817202 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24169.DS18928.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24232.DS19254.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Right.H-24232 Fetal Renal Cortex Fetal_Renal_Cortex_Right H-24232 GSM817210 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24232.DS19254.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23790.DS17381.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-23790 Fetal Renal Pelvis Fetal_Renal_Pelvis H-23790 GSM701501 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23790.DS17381.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23833.DS17451.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-23833 Fetal Renal Pelvis Fetal_Renal_Pelvis H-23833 GSM701510 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23833.DS17451.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23914.DS17760.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-23914 Fetal Renal Pelvis Fetal_Renal_Pelvis H-23914 GSM774222 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23914.DS17760.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24005.DS18088.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-24005 Fetal Renal Pelvis Fetal_Renal_Pelvis H-24005 GSM774236 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24005.DS18088.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-24078 Fetal Renal Pelvis Fetal_Renal_Pelvis H-24078 GSM817177 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24259.DS19386.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-24259 Fetal Renal Pelvis Fetal_Renal_Pelvis H-24259 GSM817218 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24259.DS19386.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24477.DS20448.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-24477 Fetal Renal Pelvis Fetal_Renal_Pelvis H-24477 GSM878662 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24477.DS20448.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-23871.DS17553.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Left.H-23871 Fetal Renal Pelvis Fetal_Renal_Pelvis_Left H-23871 GSM701520 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-23871.DS17553.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24111.DS18666.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Left.H-24111 Fetal Renal Pelvis Fetal_Renal_Pelvis_Left H-24111 GSM817193 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24111.DS18666.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24169.DS18964.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Left.H-24169 Fetal Renal Pelvis Fetal_Renal_Pelvis_Left H-24169 GSM817205 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24169.DS18964.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24232.DS19238.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Left.H-24232 Fetal Renal Pelvis Fetal_Renal_Pelvis_Left H-24232 GSM817209 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24232.DS19238.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-23871.DS17548.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Right.H-23871 Fetal Renal Pelvis Fetal_Renal_Pelvis_Right H-23871 GSM701518 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-23871.DS17548.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24111.DS18663.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Right.H-24111 Fetal Renal Pelvis Fetal_Renal_Pelvis_Right H-24111 GSM817192 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24111.DS18663.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24169.DS18961.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Right.H-24169 Fetal Renal Pelvis Fetal_Renal_Pelvis_Right H-24169 GSM817204 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24169.DS18961.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24232.DS19235.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Right.H-24232 Fetal Renal Pelvis Fetal_Renal_Pelvis_Right H-24232 GSM817208 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24232.DS19235.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Skin.ChromatinAccessibility.H-22337.DS10987.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Skin.H-22337 Fetal Skin Fetal_Skin H-22337 GSM817158 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Skin.ChromatinAccessibility.H-22337.DS10987.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24111.DS18501.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Spinal_Cord.H-24111 Fetal Spinal Cord Fetal_Spinal_Cord H-24111 GSM817189 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24111.DS18501.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24409.DS20351.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Spinal_Cord.H-24409 Fetal Spinal Cord Fetal_Spinal_Cord H-24409 GSM878661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24409.DS20351.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24493.DS20530.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Spinal_Cord.H-24493 Fetal Spinal Cord Fetal_Spinal_Cord H-24493 GSM878663 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24493.DS20530.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Spleen.ChromatinAccessibility.H-23399.DS17448.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Spleen.H-23399 Fetal Spleen Fetal_Spleen H-23399 GSM701509 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Spleen.ChromatinAccessibility.H-23399.DS17448.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23589.DS16530.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23589 Fetal Stomach Fetal_Stomach H-23589 GSM774202 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23589.DS16530.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23758.DS17172.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23758 Fetal Stomach Fetal_Stomach H-23758 GSM774212 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23758.DS17172.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23769.DS17325.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23769 Fetal Stomach Fetal_Stomach H-23769 GSM701498 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23769.DS17325.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23887.DS17659.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23887 Fetal Stomach Fetal_Stomach H-23887 GSM701521 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23887.DS17659.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23914.DS17750.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23914 Fetal Stomach Fetal_Stomach H-23914 GSM701528 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23914.DS17750.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23964.DS17878.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23964 Fetal Stomach Fetal_Stomach H-23964 GSM701538 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23964.DS17878.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24005.DS17963.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24005 Fetal Stomach Fetal_Stomach H-24005 GSM774232 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24005.DS17963.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24078.DS18389.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24078 Fetal Stomach Fetal_Stomach H-24078 GSM817173 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24078.DS18389.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24125.DS18821.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24125 Fetal Stomach Fetal_Stomach H-24125 GSM817199 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24125.DS18821.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24401 Fetal Stomach Fetal_Stomach H-24401 GSM878660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24507.DS20546.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24507 Fetal Stomach Fetal_Stomach H-24507 GSM878665 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24507.DS20546.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Testes.ChromatinAccessibility.H24198_H23640_H24042.DS18942.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Testes.H24198_H23640_H24042 Fetal Testes Fetal_Testes H24198_H23640_H24042 GSM878617 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Testes.ChromatinAccessibility.H24198_H23640_H24042.DS18942.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23589.DS16490.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23589 Fetal Thymus Fetal_Thymus H-23589 GSM665823 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23589.DS16490.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23663.DS16841.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23663 Fetal Thymus Fetal_Thymus H-23663 GSM774204 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23663.DS16841.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23769.DS17323.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23769 Fetal Thymus Fetal_Thymus H-23769 GSM701497 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23769.DS17323.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23833.DS17474.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23833 Fetal Thymus Fetal_Thymus H-23833 GSM701513 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23833.DS17474.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23964 Fetal Thymus Fetal_Thymus H-23964 GSM701537 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17876.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23964 Fetal Thymus Fetal_Thymus H-23964 GSM774230 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17876.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-24078.DS18382.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-24078 Fetal Thymus Fetal_Thymus H-24078 GSM817172 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-24078.DS18382.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-24259.DS19287.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-24259 Fetal Thymus Fetal_Thymus H-24259 GSM878627 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-24259.DS19287.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-24401.DS20335.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-24401 Fetal Thymus Fetal_Thymus H-24401 GSM878656 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-24401.DS20335.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-24409.DS20341.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-24409 Fetal Thymus Fetal_Thymus H-24409 GSM878657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-24409.DS20341.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19558.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Abdomen.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Abdomen H-24259 GSM878635 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19558.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Abdomen.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Abdomen H-24259 GSM878636 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Back.ChromatinAccessibility.H-24218.DS19233.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Back.H-24218 Fibroblast Fibroblasts_Fetal_Skin_Back H-24218 GSM878624 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Back.ChromatinAccessibility.H-24218.DS19233.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19857.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Biceps_Left.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Biceps_Left H-24259 GSM878644 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19857.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19867.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Biceps_Left.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Biceps_Left H-24259 GSM878645 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19867.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Biceps_Right.ChromatinAccessibility.H-24259.DS19745.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Biceps_Right.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Biceps_Right H-24259 GSM878642 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Biceps_Right.ChromatinAccessibility.H-24259.DS19745.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Biceps_Right.ChromatinAccessibility.H-24259.DS19761.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Biceps_Right.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Biceps_Right H-24259 GSM878643 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Biceps_Right.ChromatinAccessibility.H-24259.DS19761.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Quadriceps_Left.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Quadriceps_Left H-24259 GSM878648 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20056.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Quadriceps_Left.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Quadriceps_Left H-24259 GSM878649 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20056.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Quadriceps_Right.ChromatinAccessibility.H-24259.DS19943.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Quadriceps_Right.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Quadriceps_Right H-24259 GSM878646 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Quadriceps_Right.ChromatinAccessibility.H-24259.DS19943.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Quadriceps_Right.ChromatinAccessibility.H-24259.DS19948.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Quadriceps_Right.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Quadriceps_Right H-24259 GSM878647 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Quadriceps_Right.ChromatinAccessibility.H-24259.DS19948.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Scalp.ChromatinAccessibility.H-24259.DS19444.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Scalp.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Scalp H-24259 GSM878633 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Scalp.ChromatinAccessibility.H-24259.DS19444.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Scalp.ChromatinAccessibility.H-24259.DS19449.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Scalp.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Scalp H-24259 GSM878634 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Scalp.ChromatinAccessibility.H-24259.DS19449.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Upper_Back.ChromatinAccessibility.H-24259.DS19696.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Upper_Back.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Upper_Back H-24259 GSM878640 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Upper_Back.ChromatinAccessibility.H-24259.DS19696.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Upper_Back.ChromatinAccessibility.H-24259.DS19706.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Upper_Back.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Upper_Back H-24259 GSM878641 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Upper_Back.ChromatinAccessibility.H-24259.DS19706.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_BMP4_Derived_Mesendoderm_Cultured_Cells ES Cell Mesendoderm_Cultured_Cells NA GSM817198 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_BMP4_Derived_Mesendoderm_Cultured_Cells ES Cell Mesendoderm_Cultured_Cells NA GSM817215 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS18736.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_BMP4_Derived_Trophoblast_Cultured_Cells ES Cell Trophoblast_Cultured_Cells NA GSM878614 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS18736.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS19317.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_BMP4_Derived_Trophoblast_Cultured_Cells ES Cell Trophoblast_Cultured_Cells NA GSM878628 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS19317.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1.ChromatinAccessibility.DS18873.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1 ES Cell H1 NA GSM878616 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1.ChromatinAccessibility.DS18873.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1.ChromatinAccessibility.DS19100.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1 ES Cell H1 NA GSM878621 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1.ChromatinAccessibility.DS19100.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS20671.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_Derived_Mesenchymal_Stem_Cells ES Cell Mesenchymal_Stem_Cells NA GSM906380 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS20671.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_Derived_Mesenchymal_Stem_Cells ES Cell Mesenchymal_Stem_Cells NA GSM906381 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS18739.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_Derived_Neuronal_Progenitor_Cultured_Cells ES Cell Neuronal_Progenitor_Cultured_Cells NA GSM878615 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS18739.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS20153.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_Derived_Neuronal_Progenitor_Cultured_Cells ES Cell Neuronal_Progenitor_Cultured_Cells NA GSM906379 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS20153.twopass.merge150.wgt10.zgt2.wig.gz +UW.H9.ChromatinAccessibility.DS18517.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H9 ES Cell H9 NA GSM878612 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H9.ChromatinAccessibility.DS18517.twopass.merge150.wgt10.zgt2.wig.gz +UW.H9.ChromatinAccessibility.DS18522.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H9 ES Cell H9 NA GSM878613 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H9.ChromatinAccessibility.DS18522.twopass.merge150.wgt10.zgt2.wig.gz +UW.IMR90.ChromatinAccessibility.DS11759.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM468792 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS11759.twopass.merge150.wgt10.zgt2.wig.gz +UW.IMR90.ChromatinAccessibility.DS11764.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM468801 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS11764.twopass.merge150.wgt10.zgt2.wig.gz +UW.IMR90.ChromatinAccessibility.DS13219.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM530665 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS13219.twopass.merge150.wgt10.zgt2.wig.gz +UW.IMR90.ChromatinAccessibility.DS13229.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM530666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS13229.twopass.merge150.wgt10.zgt2.wig.gz +UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_19.11 IPS cell iPS_DF_19.11 NA GSM665801 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.twopass.merge150.wgt10.zgt2.wig.gz +UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_19.7 IPS cell iPS_DF_19.7 NA GSM665800 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.twopass.merge150.wgt10.zgt2.wig.gz +UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_4.7 IPS cell iPS_DF_4.7 NA GSM665803 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.twopass.merge150.wgt10.zgt2.wig.gz +UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_6.9 IPS cell iPS_DF_6.9 NA GSM665802 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_00738.DS13199.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_00738+ Blood CD34_Mobilised; RO_00738+ GSM530664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_00738.DS13199.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01480+ Blood CD34_Mobilised; RO_01480+ GSM530658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS12774.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01492+ Blood CD34_Mobilised; RO_01492+ GSM530659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS12774.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS14206.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01492+ Blood CD34_Mobilised; RO_01492+ GSM595919 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS14206.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01508+ Blood CD34_Mobilised; RO_01508+ GSM493386 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01517.DS14129.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01517+ Blood CD34_Mobilised; RO_01517+ GSM595917 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01517.DS14129.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01520.DS12785.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01520+ Blood CD34_Mobilised; RO_01520+ GSM530660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01520.DS12785.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01527.DS11666.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01527+ Blood CD34_Mobilised; RO_01527+ GSM493387 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01527.DS11666.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS12274.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01535+ Blood CD34_Mobilised; RO_01535+ GSM493384 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS12274.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS14197.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01535+ Blood CD34_Mobilised; RO_01535+ GSM595918 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS14197.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01536.DS12339.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01536+ Blood CD34_Mobilised; RO_01536+ GSM530652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01536.DS12339.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01549.DS12734.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01549+ Blood CD34_Mobilised; RO_01549+ GSM530657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01549.DS12734.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01562.DS13196.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01562+ Blood CD34_Mobilised; RO_01562+ GSM530663 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Placenta NA E091 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E091-H3K9me3.broadPeak.gz +E092-H3K9me3.broadPeak UW H3K9me3 E092 Fetal Stomach Fetal Stomach E092 Fetal Stomach NA E092 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E092-H3K9me3.broadPeak.gz +E093-H3K9me3.broadPeak UW H3K9me3 E093 Fetal Thymus Fetal Thymus E093 Fetal Thymus NA E093 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E093-H3K9me3.broadPeak.gz +E094-H3K9me3.broadPeak UW H3K9me3 E094 Gastric Gastric E094 Gastric NA E094 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E094-H3K9me3.broadPeak.gz +E097-H3K9me3.broadPeak UW H3K9me3 E097 Ovary Ovary E097 Ovary NA E097 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E097-H3K9me3.broadPeak.gz +E098-H3K9me3.broadPeak UW H3K9me3 E098 Pancreas Pancreas E098 Pancreas NA E098 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E098-H3K9me3.broadPeak.gz +E100-H3K9me3.broadPeak UW H3K9me3 E100 Psoas Muscle Psoas Muscle E100 Psoas Muscle NA E100 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E100-H3K9me3.broadPeak.gz +E109-H3K9me3.broadPeak UW H3K9me3 E109 Small Intestine Small Intestine E109 Small Intestine NA E109 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E109-H3K9me3.broadPeak.gz \ No newline at end of file diff --git a/database/erc2.decode b/database/erc2.decode new file mode 100644 index 0000000..5a42cc7 --- /dev/null +++ b/database/erc2.decode @@ -0,0 +1,40 @@ +file lab datatype cell tissue shortcell individual acc url +E003-DNase.hotspot.fdr0.01.broad.bed UW DHS E003 H1 Cells ES Cell E003 H1 Cells NA E003 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E003-DNase.hotspot.fdr0.01.broad.bed.gz +E004-DNase.hotspot.fdr0.01.broad.bed UW DHS E004 H1 BMP4 Derived Mesendoderm Cultured Cells ES Cell E004 H1 BMP4 Derived Mesendoderm Cultured Cells NA E004 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E004-DNase.hotspot.fdr0.01.broad.bed.gz +E005-DNase.hotspot.fdr0.01.broad.bed UW DHS E005 H1 BMP4 Derived Trophoblast Cultured Cells ES Cell E005 H1 BMP4 Derived Trophoblast Cultured Cells NA E005 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E005-DNase.hotspot.fdr0.01.broad.bed.gz +E006-DNase.hotspot.fdr0.01.broad.bed UW DHS E006 H1 Derived Mesenchymal Stem Cells ES Cell E006 H1 Derived Mesenchymal Stem Cells NA E006 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E006-DNase.hotspot.fdr0.01.broad.bed.gz +E007-DNase.hotspot.fdr0.01.broad.bed UW DHS E007 H1 Derived Neuronal Progenitor Cultured Cells ES Cell E007 H1 Derived Neuronal Progenitor Cultured Cells NA E007 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E007-DNase.hotspot.fdr0.01.broad.bed.gz +E008-DNase.hotspot.fdr0.01.broad.bed UW DHS E008 H9 Cells ES Cell E008 H9 Cells NA E008 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E008-DNase.hotspot.fdr0.01.broad.bed.gz +E017-DNase.hotspot.fdr0.01.broad.bed UW DHS E017 IMR90 fetal lung fibroblasts Cell Line Lung E017 IMR90 fetal lung fibroblasts Cell Line NA E017 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E017-DNase.hotspot.fdr0.01.broad.bed.gz +E021-DNase.hotspot.fdr0.01.broad.bed UW DHS E021 iPS DF 6.9 Cells IPS cell E021 iPS DF 6.9 Cells NA E021 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E021-DNase.hotspot.fdr0.01.broad.bed.gz +E022-DNase.hotspot.fdr0.01.broad.bed UW DHS E022 iPS DF 19.11 Cells IPS cell E022 iPS DF 19.11 Cells NA E022 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E022-DNase.hotspot.fdr0.01.broad.bed.gz +E028-DNase.hotspot.fdr0.01.broad.bed UW DHS E028 Breast variant Human Mammary Epithelial Cells Breast E028 Breast variant Human Mammary Epithelial Cells NA E028 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E028-DNase.hotspot.fdr0.01.broad.bed.gz +E029-DNase.hotspot.fdr0.01.broad.bed UW DHS E029 Primary monocytes from peripheral blood Blood E029 Primary monocytes from peripheral blood NA E029 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E029-DNase.hotspot.fdr0.01.broad.bed.gz +E032-DNase.hotspot.fdr0.01.broad.bed UW DHS E032 Primary B cells from peripheral blood Blood E032 Primary B cells from peripheral blood NA E032 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E032-DNase.hotspot.fdr0.01.broad.bed.gz +E033-DNase.hotspot.fdr0.01.broad.bed UW DHS E033 Primary T cells from cord blood Blood E033 Primary T cells from cord blood NA E033 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E033-DNase.hotspot.fdr0.01.broad.bed.gz +E034-DNase.hotspot.fdr0.01.broad.bed UW DHS E034 Primary T cells from peripheral blood Blood E034 Primary T cells from peripheral blood NA E034 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E034-DNase.hotspot.fdr0.01.broad.bed.gz +E046-DNase.hotspot.fdr0.01.broad.bed UW DHS E046 Primary Natural Killer cells from peripheral Blood E046 Primary Natural Killer cells from peripheral NA E046 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E046-DNase.hotspot.fdr0.01.broad.bed.gz +E050-DNase.hotspot.fdr0.01.broad.bed UW DHS E050 Primary hematopoietic stem cells G-CSF-mobili Blood E050 Primary hematopoietic stem cells G-CSF-mobili NA E050 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E050-DNase.hotspot.fdr0.01.broad.bed.gz +E051-DNase.hotspot.fdr0.01.broad.bed UW DHS E051 Primary hematopoietic stem cells G-CSF-mobili Blood E051 Primary hematopoietic stem cells G-CSF-mobili NA E051 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E051-DNase.hotspot.fdr0.01.broad.bed.gz +E055-DNase.hotspot.fdr0.01.broad.bed UW DHS E055 Foreskin Fibroblast Primary Cells skin01 Skin E055 Foreskin Fibroblast Primary Cells skin01 NA E055 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E055-DNase.hotspot.fdr0.01.broad.bed.gz +E056-DNase.hotspot.fdr0.01.broad.bed UW DHS E056 Foreskin Fibroblast Primary Cells skin02 Skin E056 Foreskin Fibroblast Primary Cells skin02 NA E056 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E056-DNase.hotspot.fdr0.01.broad.bed.gz +E057-DNase.hotspot.fdr0.01.broad.bed UW DHS E057 Foreskin Keratinocyte Primary Cells skin02 Skin E057 Foreskin Keratinocyte Primary Cells skin02 NA E057 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E057-DNase.hotspot.fdr0.01.broad.bed.gz +E059-DNase.hotspot.fdr0.01.broad.bed UW DHS E059 Foreskin Melanocyte Primary Cells skin01 Skin E059 Foreskin Melanocyte Primary Cells skin01 NA E059 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E059-DNase.hotspot.fdr0.01.broad.bed.gz +E080-DNase.hotspot.fdr0.01.broad.bed UW DHS E080 Fetal Adrenal Gland Fetal Adrenal Gland E080 Fetal Adrenal Gland NA E080 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E080-DNase.hotspot.fdr0.01.broad.bed.gz +E081-DNase.hotspot.fdr0.01.broad.bed UW DHS E081 Fetal Brain Male Fetal Brain E081 Fetal Brain Male NA E081 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E081-DNase.hotspot.fdr0.01.broad.bed.gz +E082-DNase.hotspot.fdr0.01.broad.bed UW DHS E082 Fetal Brain Female Fetal Brain E082 Fetal Brain Female NA E082 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E082-DNase.hotspot.fdr0.01.broad.bed.gz +E083-DNase.hotspot.fdr0.01.broad.bed UW DHS E083 Fetal Heart Fetal Heart E083 Fetal Heart NA E083 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E083-DNase.hotspot.fdr0.01.broad.bed.gz +E084-DNase.hotspot.fdr0.01.broad.bed UW DHS E084 Fetal Intestine Large Fetal Intestine Large E084 Fetal Intestine Large NA E084 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E084-DNase.hotspot.fdr0.01.broad.bed.gz +E085-DNase.hotspot.fdr0.01.broad.bed UW DHS E085 Fetal Intestine Small Feta Intestine Small E085 Fetal Intestine Small NA E085 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E085-DNase.hotspot.fdr0.01.broad.bed.gz +E086-DNase.hotspot.fdr0.01.broad.bed UW DHS E086 Fetal Kidney Fetal Kidney E086 Fetal Kidney NA E086 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E086-DNase.hotspot.fdr0.01.broad.bed.gz +E088-DNase.hotspot.fdr0.01.broad.bed UW DHS E088 Fetal Lung Fetal Lung E088 Fetal Lung NA E088 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E088-DNase.hotspot.fdr0.01.broad.bed.gz +E089-DNase.hotspot.fdr0.01.broad.bed UW DHS E089 Fetal Muscle Trunk Fetal Muscle Trunk E089 Fetal Muscle Trunk NA E089 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E089-DNase.hotspot.fdr0.01.broad.bed.gz +E090-DNase.hotspot.fdr0.01.broad.bed UW DHS E090 Fetal Muscle Leg Fetal Muscle Leg E090 Fetal Muscle Leg NA E090 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E090-DNase.hotspot.fdr0.01.broad.bed.gz +E091-DNase.hotspot.fdr0.01.broad.bed UW DHS E091 Placenta Placenta E091 Placenta NA E091 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E091-DNase.hotspot.fdr0.01.broad.bed.gz +E092-DNase.hotspot.fdr0.01.broad.bed UW DHS E092 Fetal Stomach Fetal Stomach E092 Fetal Stomach NA E092 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E092-DNase.hotspot.fdr0.01.broad.bed.gz +E093-DNase.hotspot.fdr0.01.broad.bed UW DHS E093 Fetal Thymus Fetal Thymus E093 Fetal Thymus NA E093 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E093-DNase.hotspot.fdr0.01.broad.bed.gz +E094-DNase.hotspot.fdr0.01.broad.bed UW DHS E094 Gastric Gastric E094 Gastric NA E094 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E094-DNase.hotspot.fdr0.01.broad.bed.gz +E097-DNase.hotspot.fdr0.01.broad.bed UW DHS E097 Ovary Ovary E097 Ovary NA E097 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E097-DNase.hotspot.fdr0.01.broad.bed.gz +E098-DNase.hotspot.fdr0.01.broad.bed UW DHS E098 Pancreas Pancreas E098 Pancreas NA E098 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E098-DNase.hotspot.fdr0.01.broad.bed.gz +E100-DNase.hotspot.fdr0.01.broad.bed UW DHS E100 Psoas Muscle Psoas Muscle E100 Psoas Muscle NA E100 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E100-DNase.hotspot.fdr0.01.broad.bed.gz +E109-DNase.hotspot.fdr0.01.broad.bed UW DHS E109 Small Intestine Small Intestine E109 Small Intestine NA E109 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E109-DNase.hotspot.fdr0.01.broad.bed.gz \ No newline at end of file diff --git a/database/init_db.pl b/database/init_db.pl new file mode 100644 index 0000000..7dc4a81 --- /dev/null +++ b/database/init_db.pl @@ -0,0 +1,112 @@ +#! /usr/bin/env perl +use strict; +use warnings; + +use DBI; +use Getopt::Long; + +my $db_dir = "."; +my $db_name = "eforge_1.2.db"; + + +my $help; + +my $desc = qq{init_db.pl [--db_name $db_name] [--db_dir $db_dir] + +where: + --db_name is the name of the SQLite file [def: $db_name] + --db_dir is the location of the SQLite file [def: $db_dir] + +}; + +GetOptions( + "help" => \$help, + "db_name=s" => \$db_name, + "db_dir=s" => \$db_dir, + ); + +if ($help) { + print $desc; + exit(0); +} + +my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; + + +$dbh->do("CREATE TABLE IF NOT EXISTS assembly ( + assembly_id INTEGER PRIMARY KEY AUTOINCREMENT, + species_name, + assembly_name, + UNIQUE (species_name, assembly_name))"); + + +$dbh->do("CREATE TABLE IF NOT EXISTS array ( + array_id INTEGER PRIMARY KEY AUTOINCREMENT, + array_tag UNIQUE, + array_name UNIQUE, + species_name)"); +$dbh->do("CREATE TABLE IF NOT EXISTS probe_mapping_info ( + probe_mapping_id INTEGER PRIMARY KEY AUTOINCREMENT, + array_id INTEGER NOT NULL REFERENCES array(array_id), + assembly_id INTEGER NOT NULL, + url, + UNIQUE (array_id, assembly_id))"); +$dbh->do("CREATE TABLE IF NOT EXISTS probe_mapping ( + probe_mapping_id INTEGER NOT NULL REFERENCES probe_mapping_info(probe_mapping_id), + probe_id, + chr_name, + position INTEGER, + UNIQUE (probe_mapping_id, probe_id))"); +$dbh->do("CREATE INDEX probe_mapping_idx1 on probe_mapping (position, chr_name)"); + + +$dbh->do("CREATE TABLE IF NOT EXISTS proxy_filter_info ( + array_id INTEGER NOT NULL REFERENCES array(array_id), + description, + UNIQUE(array_id))"); +$dbh->do("CREATE TABLE IF NOT EXISTS proxy_filter ( + proxy_filter_id INTEGER NOT NULL REFERENCES proxy_filter_info(proxy_filter_id), + probe_id, + proxy_probes, + UNIQUE (proxy_filter_id, probe_id))"); + + +$dbh->do("CREATE TABLE IF NOT EXISTS probe_annotation_info ( + array_id INTEGER NOT NULL REFERENCES array(array_id), + gene_reference_name NOT NULL, + cgi_reference_name NOT NULL, + url, + UNIQUE(array_id))"); +$dbh->do("CREATE TABLE IF NOT EXISTS probe_annotation ( + array_id INTEGER NOT NULL REFERENCES probe_annotation_info(array_id), + probe_id NOT NULL, + gene_group, + cgi_group, + UNIQUE (array_id, probe_id))"); + + +$dbh->do("CREATE TABLE IF NOT EXISTS dataset ( + dataset_id INTEGER PRIMARY KEY AUTOINCREMENT, + dataset_tag UNIQUE, + dataset_name UNIQUE, + species_name)"); +$dbh->do("CREATE TABLE IF NOT EXISTS sample ( + dataset_id INTEGER REFERENCES dataset(dataset_id), + sample_order INTEGER, + file, + lab, + datatype, + cell, + tissue, + shortcell, + individual, + acc, + url)"); +$dbh->do("CREATE TABLE IF NOT EXISTS probe_bitstring ( + array_id INTEGER NOT NULL REFERENCES array(array_id), + probe_id INTEGER NOT NULL, + dataset_id INTEGER NOT NULL REFERENCES dataset(dataset_id), + sum INTEGER, + bit, + UNIQUE(array_id,probe_id,dataset_id))"); diff --git a/database/load_27k_array.pl b/database/load_27k_array.pl new file mode 100644 index 0000000..c5e8011 --- /dev/null +++ b/database/load_27k_array.pl @@ -0,0 +1,346 @@ +#! /usr/bin/env perl +use strict; +use warnings; + +use Getopt::Long; +use File::Spec qw(splitpath); +use DBI; + +my $db_dir = "."; +my $db_name = "eforge_1.2.db"; +my $array_tag = "27k"; +my $array_name = "Illumina Human 27k array (subset of 450k only)"; +my $species = "Homo sapiens"; +my $proxy_threshold = 1000; +my $illumina27k_bpm_file = 'ftp://webdata:webdata@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation27/humanmethylation27_270596_v1-2.bpm'; +my $illumina450k_csv_file = 'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation450/HumanMethylation450_15017482_v1-2.csv'; +my $work_dir = "."; +my $bedtools = "bedtools"; + +my $help; + +my $desc = qq{load_27k_array.pl [options] + +DESCRIPTION: + +This script loads the subset of probe locations and annotations of the Illumina Human 27k +methylation array that are shared with the 450k array into the eFORGE database. + +Note that you *must* load the arrays before loading the datasets. If you want to include new arrays +at a later date, you will have to reload all the datasets again (i.e. you will have to re-start from +scratch). + +Optional arguments: + --db_name + is the name of the SQLite file [def: $db_name] + --db_dir + is the location of the SQLite file [def: $db_dir] + --work_dir + is the location where temporary files will be downloaded/created [def: $work_dir] + --bedtools + is the name of the bedtools executable you want to use [def: $bedtools] +}; + +GetOptions( + "help" => \$help, + "db_name=s" => \$db_name, + "db_dir=s" => \$db_dir, + "work_dir=s" => \$work_dir, + "bedtools=s" => \$bedtools, + ); + +my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; + +my ($vol, $path, $file) = File::Spec->splitpath($illumina450k_csv_file); + +if (!-e "$work_dir/$file") { + download_url($illumina450k_csv_file, $work_dir); +} + +my $array450k_info = parse_450k_file("$work_dir/$file"); + +my ($vol27k, $path27k, $file27k) = File::Spec->splitpath($illumina27k_bpm_file); + +if (!-e "$work_dir/$file27k") { + download_url($illumina27k_bpm_file, $work_dir); +} + +my $array27k_info = parse_27k_file("$work_dir/$file27k"); + +my $array_info = subset_array($array450k_info, $array27k_info); + +load_array($dbh, $db_name, $species, $array_tag, $array_name, $array_info); + +load_proxy_filter($dbh, $db_name, $array_tag, "GRCh37", $work_dir, $proxy_threshold); + +exit(); + + +sub download_url { + my ($url, $work_dir) = @_; + + print "Downloading $url...\n"; + system("wget -q -N -P $work_dir $url"); +} + + +sub parse_450k_file { + my ($illumina450k_csv_file) = @_; + my $array; + + open(CSV, $illumina450k_csv_file) or die; + my $annotation; + my @gene_annotations = ("TSS200", "TSS1500", "1stExon", "Body", "3'UTR", "5'UTR", "IGR"); + my $cpg_annotations = { + 'N_Shelf' => "Shelf_Shore", + 'S_Shelf' => "Shelf_Shore", + 'N_Shore' => "Shelf_Shore", + 'S_Shore' => "Shelf_Shore", + 'Island' => "Island"}; + while () { + chomp; + my @data = split(",", $_); + my $probe_id = $data[0]; + next if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./); + my $probe_chr37 = $data[11]; + my $probe_loc37 = $data[12]; + my $probe_chr36 = $data[14]; + my $probe_loc36 = $data[15]; + my $this_gene_annotation_arrayStr = $data[23]; + my $this_cpg_annotation = $data[25]?$cpg_annotations->{$data[25]}:"NA"; + + my $this_gene_annotation; + if (!defined($this_gene_annotation_arrayStr) or $this_gene_annotation_arrayStr eq "") { + $this_gene_annotation = "IGR"; + } else { + my @this_gene_annotations = split(";", $this_gene_annotation_arrayStr); + foreach my $this_a (@this_gene_annotations) { + if (grep {$_ eq $this_a} @gene_annotations) { + $this_gene_annotation = $this_a; + last; + } + } + } + + $annotation->{$this_gene_annotation."-".$this_cpg_annotation}++; + + $array->{$probe_id} = [$probe_chr36, $probe_loc36, $probe_chr37, $probe_loc37, $this_gene_annotation, $this_cpg_annotation]; + } + close(CSV); +# foreach my $this_a (keys %$annotation) { #@gene_annotations) { +# print $annotation->{$this_a}, "\t", $this_a, "\n"; +# } + + return $array; +} + + +sub parse_27k_file { + my ($illumina27k_bpm_file) = @_; + my $array; + + open(CSV, $illumina27k_bpm_file) or die; + my $block = ""; + while () { + if (/^\[(\w+)\]/) { + $block = $1; + } + next if ($block ne "Assay"); + + chomp; + my @data = split(",", $_); + my $probe_id = $data[0]; + my $name = $data[1]; + my $probe_chr36 = $data[8]; + my $probe_loc36 = $data[9]; + + if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./) { +# print "Skipping $probe_id\n"; + next; + } + if ($probe_id ne $name) { + print "ERROR: $probe_id ne $name\n"; + } + $array->{$probe_id} = [$probe_chr36, $probe_loc36]; + } + close(CSV); + + return $array; +} + +sub subset_array { + my ($full_array, $sub_array) = @_; + my $array; + foreach my $probe_id (keys %$full_array) { + if ($sub_array->{$probe_id}) { + $array->{$probe_id} = $full_array->{$probe_id}; + print "MISMATCH $probe_id\n" if (($full_array->{$probe_id}->[0] ne $sub_array->{$probe_id}->[0]) + or + ($full_array->{$probe_id}->[1] != $sub_array->{$probe_id}->[1])); + } + } + return $array; +} + + +sub load_array_1 { + my ($dbh, $code_name, $array_info) = @_; + + my $table_name = $code_name; + $table_name =~ s/\W//g; + $table_name = "array_$table_name"; + $dbh->do("CREATE TABLE IF NOT EXISTS $table_name (probe_id, location, gene_group, cgi_group)"); + + my $sth = $dbh->prepare("INSERT INTO array_$code_name VALUES (?, ?, ?, ?)"); + foreach my $this_probe_id (sort keys $array_info) { + my ($chr, $loc, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}}; + my $location = "$chr:$loc-$loc"; + $sth->execute($this_probe_id, $location, $gene_group, $cgi_group); + } + $sth->finish(); + + return $table_name; +} + + +sub load_array { + my ($dbh, $db_name, $species_name, $array_tag, $array_name, $array_info) = @_; + + my $sth; + $sth = $dbh->prepare("INSERT OR IGNORE INTO array (array_tag, array_name, species_name) VALUES (?, ?, ?)"); + $sth->execute($array_tag, $array_name, $species_name); + my $array_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + if ($array_id == 0) { + $array_id = $dbh->selectrow_array("SELECT array_id FROM array WHERE array_name = '$array_name' AND species_name = 'Homo sapiens'"); + } + + $sth = $dbh->prepare("INSERT OR IGNORE INTO assembly (species_name, assembly_name) VALUES (?, ?)"); + $sth->execute($species_name, "GRCh37"); + $sth->execute($species_name, "NCBI36"); + $sth->finish(); + my $human36_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'NCBI36'"); + my $human37_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'GRCh37'"); + + $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping_info (array_id, assembly_id, url) VALUES (?, ?, ?)"); + $sth->execute($array_id, $human36_assembly_id, ""); + my $probe_mapping_human36_id = $dbh->last_insert_id("", "", "", ""); + $sth->execute($array_id, $human37_assembly_id, ""); + my $probe_mapping_human37_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + + $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation_info (array_id, gene_reference_name, cgi_reference_name, url) VALUES (?, ?, ?, ?)"); + $sth->execute($array_id, "RefSeq", "UCSC CpG Islands", ""); +# my $probe_annotation_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + + open(CSV1, ">probe_mapping.csv") or die; + open(CSV2, ">probe_annotation.csv") or die; +# my $sth1 = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping (probe_mapping_id, probe_id, chr_name, position) VALUES (?, ?, ?, ?)"); +# my $sth2 = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation (probe_annotation_id, probe_id, gene_group, cgi_group) VALUES (?, ?, ?, ?)"); + foreach my $this_probe_id (sort keys $array_info) { + my ($chr36, $loc36, $chr37, $loc37, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}}; + print CSV1 join(",", $probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36), "\n"; + print CSV1 join(",", $probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37), "\n"; +# print CSV2 join(",", $probe_annotation_id, $array_id, $this_probe_id, $gene_group, $cgi_group), "\n"; + print CSV2 join(",", $array_id, $this_probe_id, $gene_group, $cgi_group), "\n"; +# $sth1->execute($probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36) if ($probe_mapping_human36_id); +# $sth1->execute($probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37) if ($probe_mapping_human37_id); +# $sth2->execute($probe_annotation_id, $this_probe_id, $gene_group, $cgi_group) if ($probe_annotation_id); + } + close(CSV1); + close(CSV2); + system("echo '.mode csv +.import probe_mapping.csv probe_mapping +.import probe_annotation.csv probe_annotation' | sqlite3 $db_name"); +# $sth1->finish(); +# $sth2->finish(); + +} + +sub load_proxy_filter { + my ($dbh, $db_name, $array_tag, $assembly_name, $work_dir, $distance_threshold) = @_; + + my $array_id = $dbh->selectrow_arrayref("SELECT array_id FROM array WHERE array_tag = '$array_tag'")->[0]; + my $bed_file = dump_array_bed_file($dbh, $array_id, $assembly_name, $work_dir); + my $this_output_bed_file = "$work_dir/array_${array_id}.proxy.bed"; + my $runstr = "$bedtools window -w $distance_threshold -a $bed_file -b $bed_file > $this_output_bed_file"; + system($runstr) == 0 or die "Error while running bedtools: $?"; + + my $sth = $dbh->prepare("INSERT OR IGNORE INTO proxy_filter_info (array_id, description) VALUES (?, ?)"); + $sth->execute($array_id, "Distance-based: 1kb"); + + open(BED, $this_output_bed_file) or die; + my $all_probes; + my $mapping_probes; + while () { + chomp; + my ($chr1, $start1, $end1, $probe1, $chr2, $start2, $end2, $probe2) = split("\t", $_); + $all_probes->{$probe1} = 1; + if ($probe1 ne $probe2) { + $mapping_probes->{$probe1}->{$probe2} = 1; + } + } + close(BED); + open(CSV, ">proxy_filter.csv") or die; + foreach my $probe (sort keys %$all_probes) { + if (defined($mapping_probes->{$probe})) { + print CSV "$array_id,$probe,", join("|", sort keys %{$mapping_probes->{$probe}}), "\n"; + } else { + print CSV "$array_id,$probe,NONE\n"; + } + } + close(CSV); + system("echo '.mode csv +.import proxy_filter.csv proxy_filter' | sqlite3 $db_name"); + +} + +sub dump_array_bed_file { + my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_; + my $sql = "SELECT probe_mapping_id + FROM probe_mapping_info + JOIN assembly USING (assembly_id) + WHERE array_id = $this_array_id + AND assembly_name = '$assembly_name'"; + my $probe_mapping_id = $dbh->selectrow_array($sql); + if (!$probe_mapping_id) { + die "Cannot find a mapping for array $this_array_id and assembly $assembly_name\n"; + } + + $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id"; + my $probes = $dbh->selectall_arrayref($sql); + + my $bed_file = "$work_dir/array_${this_array_id}.bed"; + open(BED, ">$bed_file") or die; + foreach my $this_probe (sort _sort_probes @$probes) { + print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n"; + } + close(BED); + + return $bed_file; +} + +sub _sort_probes { + my $chr_a = $a->[1]; + my $chr_b = $b->[1]; + my $loc_a = $a->[2]; + my $loc_b = $b->[2]; + $chr_a =~ s/chr//; + $chr_b =~ s/chr//; + if ($chr_a eq $chr_b) { + return $loc_a <=> $loc_b; + } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) { + return $chr_a <=> $chr_b; + } elsif ($chr_a =~ /^\d/) { + return -1; + } elsif ($chr_b =~ /^\d/) { + return 1; + } else { + return $chr_a cmp $chr_b; + } +} + + +exit(); diff --git a/database/load_450k_array.pl b/database/load_450k_array.pl new file mode 100644 index 0000000..3dadd80 --- /dev/null +++ b/database/load_450k_array.pl @@ -0,0 +1,287 @@ +#! /usr/bin/env perl +use strict; +use warnings; + +use Getopt::Long; +use File::Spec qw(splitpath); +use DBI; + +my $db_dir = "."; +my $db_name = "eforge_1.2.db"; +my $array_tag = "450k"; +my $array_name = "Illumina Human 450k array"; +my $species = "Homo sapiens"; +my $proxy_threshold = 1000; +my $illumina450k_csv_file = 'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation450/HumanMethylation450_15017482_v1-2.csv'; +my $work_dir = "."; +my $bedtools = "bedtools"; + +my $help; + +my $desc = qq{load_450k_array.pl [options] + +DESCRIPTION: + +This script loads the probe locations and annotations of the Illumina Human 450k methylation array +into the eFORGE database. + +Note that you *must* load the arrays before loading the datasets. If you want to include new arrays +at a later date, you will have to reload all the datasets again (i.e. you will have to re-start from +scratch). + +Optional arguments: + --db_name + is the name of the SQLite file [def: $db_name] + --db_dir + is the location of the SQLite file [def: $db_dir] + --work_dir + is the location where temporary files will be downloaded/created [def: $work_dir] + --bedtools + is the name of the bedtools executable you want to use [def: $bedtools] +}; + +GetOptions( + "help" => \$help, + "db_name=s" => \$db_name, + "db_dir=s" => \$db_dir, + "work_dir=s" => \$work_dir, + "bedtools=s" => \$bedtools, + ); + +my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; + +my ($vol, $apth, $file) = File::Spec->splitpath($illumina450k_csv_file); + +if (!-e "$work_dir/$file") { + download_url($illumina450k_csv_file, $work_dir); +} + +my $array_info = parse_450k_file("$work_dir/$file"); + +load_array($dbh, $db_name, $species, $array_tag, $array_name, $array_info); + +load_proxy_filter($dbh, $db_name, $array_tag, "GRCh37", $work_dir, $proxy_threshold); + +exit(); + + +sub download_url { + my ($url, $work_dir) = @_; + + print "Downloading $url...\n"; + system("wget -q -N -P $work_dir $url"); +} + + +sub parse_450k_file { + my ($illumina450k_csv_file) = @_; + my $array; + + open(CSV, $illumina450k_csv_file) or die; + my $annotation; + my @gene_annotations = ("TSS200", "TSS1500", "1stExon", "Body", "3'UTR", "5'UTR", "IGR"); + my $cpg_annotations = { + 'N_Shelf' => "Shelf_Shore", + 'S_Shelf' => "Shelf_Shore", + 'N_Shore' => "Shelf_Shore", + 'S_Shore' => "Shelf_Shore", + 'Island' => "Island"}; + while () { + chomp; + my @data = split(",", $_); + my $probe_id = $data[0]; + next if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./); + my $probe_chr37 = $data[11]; + my $probe_loc37 = $data[12]; + my $probe_chr36 = $data[14]; + my $probe_loc36 = $data[15]; + my $this_gene_annotation_arrayStr = $data[23]; + my $this_cpg_annotation = $data[25]?$cpg_annotations->{$data[25]}:"NA"; + + my $this_gene_annotation; + if (!defined($this_gene_annotation_arrayStr) or $this_gene_annotation_arrayStr eq "") { + $this_gene_annotation = "IGR"; + } else { + my @this_gene_annotations = split(";", $this_gene_annotation_arrayStr); + foreach my $this_a (@this_gene_annotations) { + if (grep {$_ eq $this_a} @gene_annotations) { + $this_gene_annotation = $this_a; + last; + } + } + } + + $annotation->{$this_gene_annotation."-".$this_cpg_annotation}++; + + $array->{$probe_id} = [$probe_chr36, $probe_loc36, $probe_chr37, $probe_loc37, $this_gene_annotation, $this_cpg_annotation]; + } + close(CSV); +# foreach my $this_a (keys %$annotation) { #@gene_annotations) { +# print $annotation->{$this_a}, "\t", $this_a, "\n"; +# } + + return $array; +} + + +sub load_array_1 { + my ($dbh, $code_name, $array_info) = @_; + + my $table_name = $code_name; + $table_name =~ s/\W//g; + $table_name = "array_$table_name"; + $dbh->do("CREATE TABLE IF NOT EXISTS $table_name (probe_id, location, gene_group, cgi_group)"); + + my $sth = $dbh->prepare("INSERT INTO array_$code_name VALUES (?, ?, ?, ?)"); + foreach my $this_probe_id (sort keys $array_info) { + my ($chr, $loc, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}}; + my $location = "$chr:$loc-$loc"; + $sth->execute($this_probe_id, $location, $gene_group, $cgi_group); + } + $sth->finish(); + + return $table_name; +} + + +sub load_array { + my ($dbh, $db_name, $species_name, $array_tag, $array_name, $array_info) = @_; + + my $sth; + $sth = $dbh->prepare("INSERT OR IGNORE INTO array (array_tag, array_name, species_name) VALUES (?, ?, ?)"); + $sth->execute($array_tag, $array_name, $species_name); + my $array_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + if ($array_id == 0) { + $array_id = $dbh->selectrow_array("SELECT array_id FROM array WHERE array_name = '$array_name' AND species_name = 'Homo sapiens'"); + } + + $sth = $dbh->prepare("INSERT OR IGNORE INTO assembly (species_name, assembly_name) VALUES (?, ?)"); + $sth->execute($species_name, "GRCh37"); + $sth->execute($species_name, "NCBI36"); + $sth->finish(); + my $human36_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'NCBI36'"); + my $human37_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'GRCh37'"); + + $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping_info (array_id, assembly_id, url) VALUES (?, ?, ?)"); + $sth->execute($array_id, $human36_assembly_id, ""); + my $probe_mapping_human36_id = $dbh->last_insert_id("", "", "", ""); + $sth->execute($array_id, $human37_assembly_id, ""); + my $probe_mapping_human37_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + + $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation_info (array_id, gene_reference_name, cgi_reference_name, url) VALUES (?, ?, ?, ?)"); + $sth->execute($array_id, "RefSeq", "UCSC CpG Islands", ""); +# my $probe_annotation_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + + open(CSV1, ">probe_mapping.csv") or die; + open(CSV2, ">probe_annotation.csv") or die; +# my $sth1 = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping (probe_mapping_id, probe_id, chr_name, position) VALUES (?, ?, ?, ?)"); +# my $sth2 = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation (probe_annotation_id, probe_id, gene_group, cgi_group) VALUES (?, ?, ?, ?)"); + foreach my $this_probe_id (sort keys $array_info) { + my ($chr36, $loc36, $chr37, $loc37, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}}; + print CSV1 join(",", $probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36), "\n"; + print CSV1 join(",", $probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37), "\n"; +# print CSV2 join(",", $probe_annotation_id, $array_id, $this_probe_id, $gene_group, $cgi_group), "\n"; + print CSV2 join(",", $array_id, $this_probe_id, $gene_group, $cgi_group), "\n"; +# $sth1->execute($probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36) if ($probe_mapping_human36_id); +# $sth1->execute($probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37) if ($probe_mapping_human37_id); +# $sth2->execute($probe_annotation_id, $this_probe_id, $gene_group, $cgi_group) if ($probe_annotation_id); + } + close(CSV1); + close(CSV2); + system("echo '.mode csv +.import probe_mapping.csv probe_mapping +.import probe_annotation.csv probe_annotation' | sqlite3 $db_name"); +# $sth1->finish(); +# $sth2->finish(); + +} + +sub load_proxy_filter { + my ($dbh, $db_name, $array_tag, $assembly_name, $work_dir, $distance_threshold) = @_; + + my $array_id = $dbh->selectrow_arrayref("SELECT array_id FROM array WHERE array_tag = '$array_tag'")->[0]; + my $bed_file = dump_array_bed_file($dbh, $array_id, $assembly_name, $work_dir); + my $this_output_bed_file = "$work_dir/array_${array_id}.proxy.bed"; + my $runstr = "$bedtools window -w $distance_threshold -a $bed_file -b $bed_file > $this_output_bed_file"; + system($runstr) == 0 or die "Error while running bedtools: $?"; + + my $sth = $dbh->prepare("INSERT OR IGNORE INTO proxy_filter_info (array_id, description) VALUES (?, ?)"); + $sth->execute($array_id, "Distance-based: 1kb"); + + open(BED, $this_output_bed_file) or die; + my $all_probes; + my $mapping_probes; + while () { + chomp; + my ($chr1, $start1, $end1, $probe1, $chr2, $start2, $end2, $probe2) = split("\t", $_); + $all_probes->{$probe1} = 1; + if ($probe1 ne $probe2) { + $mapping_probes->{$probe1}->{$probe2} = 1; + } + } + close(BED); + open(CSV, ">proxy_filter.csv") or die; + foreach my $probe (sort keys %$all_probes) { + if (defined($mapping_probes->{$probe})) { + print CSV "$array_id,$probe,", join("|", sort keys %{$mapping_probes->{$probe}}), "\n"; + } else { + print CSV "$array_id,$probe,NONE\n"; + } + } + close(CSV); + system("echo '.mode csv +.import proxy_filter.csv proxy_filter' | sqlite3 $db_name"); + +} + +sub dump_array_bed_file { + my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_; + my $sql = "SELECT probe_mapping_id + FROM probe_mapping_info + JOIN assembly USING (assembly_id) + WHERE array_id = $this_array_id + AND assembly_name = '$assembly_name'"; + my $probe_mapping_id = $dbh->selectrow_array($sql); + if (!$probe_mapping_id) { + die "Cannot find a mapping for array $this_array_id and assembly $assembly_name\n"; + } + + $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id"; + my $probes = $dbh->selectall_arrayref($sql); + + my $bed_file = "$work_dir/array_${this_array_id}.bed"; + open(BED, ">$bed_file") or die; + foreach my $this_probe (sort _sort_probes @$probes) { + print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n"; + } + close(BED); + + return $bed_file; +} + +sub _sort_probes { + my $chr_a = $a->[1]; + my $chr_b = $b->[1]; + my $loc_a = $a->[2]; + my $loc_b = $b->[2]; + $chr_a =~ s/chr//; + $chr_b =~ s/chr//; + if ($chr_a eq $chr_b) { + return $loc_a <=> $loc_b; + } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) { + return $chr_a <=> $chr_b; + } elsif ($chr_a =~ /^\d/) { + return -1; + } elsif ($chr_b =~ /^\d/) { + return 1; + } else { + return $chr_a cmp $chr_b; + } +} + + +exit(); diff --git a/database/load_dataset.pl b/database/load_dataset.pl new file mode 100644 index 0000000..6c947d3 --- /dev/null +++ b/database/load_dataset.pl @@ -0,0 +1,416 @@ +#! /usr/bin/env perl +use strict; +use warnings; + +use Getopt::Long; +use DBI; + +my $db_dir = "."; +my $db_name = "eforge_1.1.db"; +my $dataset_name = "ENCODE"; +my $dataset_tag = "encode"; +my $decode_file = "encode.decode"; +my $work_dir = "/tmp"; +my $species_name = "Homo sapiens"; +my $assembly_name = "GRCh37"; +my $bedtools = "bedtools"; + +my $help; + +my $desc = qq{load_dataset.pl [options] + +DESCRIPTION: + +This script reads a 'decode' file which contains references to a list of samples, each of them +corresponding to a given dataset. Each of these files is a BED or BED-like file that is read by +bedtools to find overlaps with each and every array loaded in the eFORGE database. + +Note that you *must* load the arrays first. If you want to include new arrays at a later date, you +will have to reload all the datasets again (i.e. you will have to re-start from scratch). + +Required parameters: + --tag or --dataset_tag + the ID for this database. This needs to be unique. + --name or --dataset_name + the name for this database. This can be a longer description. It will be used in the web interface. + --decode_file + the file with the information about each sample in this dataset + +Optional parameters: + --db_name + is the name of the SQLite file [def: $db_name] + --db_dir + is the location of the SQLite file [def: $db_dir] + --work_dir + is the location where temporary files will be downloaded/created [def: $work_dir] + --bedtools + is the name of the bedtools executable you want to use [def: $bedtools] + --species + is the name of the species [def: $species_name] + --assembly + is the name of the assembly [def: $assembly_name] +}; + +GetOptions( + "help" => \$help, + "db_name=s" => \$db_name, + "db_dir=s" => \$db_dir, + "tag|dataset_tag=s" => \$dataset_tag, + "name|dataset_name=s" => \$dataset_name, + "decode_file=s" => \$decode_file, + "work_dir=s" => \$work_dir, + "species=s" => \$species_name, + "assembly=s" => \$assembly_name, + ); + +if ($help) { + print $desc; + exit(0); +} + +my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; + +system("mkdir -p $work_dir"); + +my $decode_table = get_decode_table($decode_file); + +my $dataset_id = load_dataset($dbh, $species_name, $decode_table, $dataset_name, $dataset_tag); + +download_bed_files($decode_table, $work_dir); + +my $arrays = get_all_arrays_for_species($dbh, $species_name); + +foreach my $this_array (@$arrays) { + my ($this_array_id, $this_array_name) = @$this_array; + my $sorted_array_bed_file = dump_array_bed_file($dbh, $this_array_id, $assembly_name, $work_dir); + my $single_overlaps_bed_files = run_single_overlap_bedtools($bedtools, $work_dir, $sorted_array_bed_file, $decode_table, $this_array_id, $this_array_name); + my $concatenated_overlaps_bed_file = paste_files($single_overlaps_bed_files, $work_dir, $this_array_id); + my $final_overlaps_bed_file = add_sum_column_to_concatenated_bedfile($concatenated_overlaps_bed_file, $work_dir, $this_array_id); + load_bitstrings($dbh, $db_name, $final_overlaps_bed_file, $this_array_id, $dataset_id); +} + +# + + +exit(); + +my $input_bed_files = get_input_bed_files_from_decode_table($decode_file); + +exit(0); + +sub load_dataset { + my ($dbh, $species_name, $decode_table, $dataset_name) = @_; + my $dataset_id; + + my $sth; + $sth = $dbh->prepare("INSERT OR IGNORE INTO dataset (dataset_tag, dataset_name, species_name) VALUES (?, ?, ?)"); + $sth->execute($dataset_tag, $dataset_name, $species_name); + $dataset_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + if ($dataset_id == 0) { + $dataset_id = $dbh->selectrow_array("SELECT dataset_id FROM dataset WHERE dataset_name = '$dataset_name' AND species_name = '$species_name'"); + } + + + $sth = $dbh->prepare("INSERT OR IGNORE INTO sample (dataset_id, sample_order, file, lab, datatype, cell, tissue, shortcell, individual, acc, url) + VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)"); + my $sample_order = 1; + foreach my $this_sample (@$decode_table) { + $sth->execute($dataset_id, + $sample_order, + $this_sample->{file}, + $this_sample->{lab}, + $this_sample->{datatype}, + $this_sample->{cell}, + $this_sample->{tissue}, + $this_sample->{shortcell}, + $this_sample->{individual}, + $this_sample->{acc}, + $this_sample->{url}); + $sample_order++; + } + + return($dataset_id); +} + +sub load_bitstrings { + my ($dbh, $db_name, $bed_file, $array_id, $dataset_id) = @_; + +# my $sql = "INSERT INTO probe_bitstring (array_id, probe_id, dataset_id, sum, bit) +# VALUES (?, ?, ?, ?, ?)"; +# my $sth = $dbh->prepare($sql); + open(BED, $bed_file) or die "Cannot open BED file <$bed_file>\n"; + open(CSV, ">probe_bitstring.csv") or die "Cannot open CVS temporary file \n"; + while() { + chomp; + my ($chr, $start, $end, $probe_id, $sum, $bitstring) = split("\t", $_); + print CSV join(",", $array_id, $probe_id, $dataset_id, $sum, $bitstring), "\n"; +# $sth->execute($array_id, $probe_id, $dataset_id, $sum, $bitstring); + } + close(BED); + close(CSV); + system("echo '.mode csv +.import probe_bitstring.csv probe_bitstring' | sqlite3 $db_name"); +# $sth->finish(); +} + +=head2 add_sum_column_to_concatenated_bedfile + + Arg[1] : string $concatenated_overlaps_bed_file (location of the input BED file with 0/1 flags on the 4th column) + Arg[2] : string $work_dir (where to put the temporary files) + Example : my $final_overlaps_bed_file = add_sum_column_to_concatenated_bedfile($concatenated_overlaps_bed_file, $work_dir); + Description : Reads the input BED file ($concatenated_overlaps_bed_file) which contains a series + of 0 and 1 flags in the 4th column. This function reads the number of ones in that + column and include that value in the output BED file. The output BED file will + contain that number in the 4th column and the series of flag in the 5th colum. + Returns : string $final_overlaps_bed_file (the location of the resulting BED file) + Exceptions : Dies if error when opening the files + +=cut + +sub add_sum_column_to_concatenated_bedfile { + my ($concatenated_overlaps_bed_file, $work_dir, $array_id) = @_; + my $final_overlaps_bed_file = "$work_dir/final_overlaps.array_${array_id}.bed"; + + open(BED_IN, $concatenated_overlaps_bed_file) or die "Cannot open BED file <$concatenated_overlaps_bed_file>\n"; + open(BED_OUT, ">$final_overlaps_bed_file") or die "Cannot open BED file <$final_overlaps_bed_file>\n"; + while() { + chomp; + my ($this_chr, $this_start, $this_end, $this_probe, $this_bitstring) = split("\t", $_); + my $num = $this_bitstring =~ tr/1/1/; + print BED_OUT join("\t", $this_chr, $this_start, $this_end, $this_probe, $num, $this_bitstring), "\n"; + } + close(BED_IN); + close(BED_OUT); + + return $final_overlaps_bed_file; +} + + +=head2 run_single_overlap_bedtools + + Arg[1] : string $bedtools (either full path or just the binary if in the $PATH) + Arg[2] : string $work_dir (where to put the temporary files) + Arg[3] : string $sorted_450k_bed_file (location of the BED file with sorted 450K features) + Arg[4] : arrayref of hash $decode_table + Example : my $single_overlaps_bed_files = run_single_overlap_bedtools($bedtools, $work_dir, $sorted_450k_bed_file, $decode_table); + Description : Run bedtools on the sorted 450K features vs all the BED DNAse features, one at a time. + Returns : arrayref of string $total_overlaps_bed_files (the locations of the resulting BED files) + Exceptions : Dies if error when running bedtools + +=cut + +sub run_single_overlap_bedtools { + my ($bedtools, $work_dir, $sorted_array_bed_file, $decode_table, $array_id, $array_name) = @_; + my $single_overlap_bed_files = []; + + foreach my $this_input_bed_file (map {$_->{"file"}} @$decode_table) { + print "Overlap between $array_name and $this_input_bed_file...\n"; + my $this_output_bed_file = $this_input_bed_file; + $this_output_bed_file =~ s/.+\///; + $this_output_bed_file = "$work_dir/single_overlaps.array_${array_id}.$this_output_bed_file"; + my $runstr = "$bedtools intersect -c -a $sorted_array_bed_file -b $work_dir/$this_input_bed_file > $this_output_bed_file"; + system($runstr) == 0 or die "Error while running bedtools: $?"; + push(@$single_overlap_bed_files, $this_output_bed_file); + } + + return $single_overlap_bed_files; +} + + +sub get_decode_table { + my ($decode_file) = @_; + my $decode_table; + + open(DECODE, $decode_file) or die "Cannot open decode file <$decode_file>\n"; + my $whole_text = join("\n", ); + $whole_text =~ s/[\r\n]+/\n/g; + my @lines = split("\n", $whole_text); + close(DECODE); + + my @header = split("\t", shift(@lines)); + + foreach my $this_line (@lines) { + my @data = split("\t", $this_line); + my $decode_record = {}; + for (my $i=0; $i<@header; $i++) { + $decode_record->{$header[$i]} = $data[$i]; + } + # Check that file and URL match + die "File: ".$decode_record->{"file"}."\nURL: ".$decode_record->{"url"}."\nOn line: $this_line" + if ($decode_record->{"url"} !~ $decode_record->{"file"}); + $decode_record->{"file"} = $decode_record->{"url"}; + $decode_record->{"file"} =~ s/.+\///g; + push(@$decode_table, $decode_record); + } + + return $decode_table; +} + +sub download_bed_files { + my ($decode_table, $work_dir) = @_; + + foreach my $this_decode_entry (@$decode_table) { + my $url = $this_decode_entry->{"url"}; + my $file = $this_decode_entry->{"file"}; + if (!-e "$work_dir/$file") { + download_url($url, $work_dir); + } + } +} + + +sub download_url { + my ($url, $work_dir) = @_; + + print "Downloading $url...\n"; + system("wget", "-q", "-N", "-P", $work_dir, $url) == 0 + or die "Error: wget -q -N -P $work_dir $url\n$!"; +} + + +sub paste_files { + my ($files, $work_dir, $array_id) = @_; + my $output_file = "$work_dir/concat_overlaps.array_${array_id}.bed"; + + my $max_num_files = 200; + my $c = 0; + my $temp_output_file; + my @original_files = @$files; + while (@$files > 1) { + $c++; + $temp_output_file = "$work_dir/temp.$$.$c.paste_files.txt"; + my $input_files = [splice(@$files, 0, $max_num_files)]; +# print STDERR "Merging ", join(", ", @$input_files), " into $temp_output_file\n"; + merge_files($temp_output_file, $input_files); + unshift(@$files, $temp_output_file); + } + rename($temp_output_file, $output_file); + + unlink glob "$work_dir/temp.$$.*.paste_files.txt"; + +# +# +# +# +# unlink @original_files; +# +# +# +# + + return $output_file; +} + + +sub merge_files { + my ($output_file, $input_files) = @_; + my @fhs; + my $c = 0; + + foreach my $this_input_file (@$input_files) { + open($fhs[$c++], $this_input_file) or die "Cannot open $this_input_file: $!\n"; + } + open(OUT, ">$output_file") or die "Cannot open $output_file: $!\n"; + + my $first_fh = shift(@fhs); + + while (1) { + my $line = <$first_fh>; + chomp($line); + my ($chr, $start, $end, $probe_id, $value) = split("\t", $line); + print OUT join("\t", $chr, $start, $end, $probe_id, $value); + foreach my $this_fh (@fhs) { + my $line = <$this_fh>; + chomp($line); + my ($this_chr, $this_start, $this_end, $this_probe_id, $this_value) = split("\t", $line); + if (($this_chr ne $chr) or ($this_start != $start) or ($this_end != $end) or ($this_probe_id ne $probe_id)) { + die "Files do not contain the same $chr-$start-$end-$probe_id lines\n"; + } + print OUT $this_value; + } + print OUT "\n"; + if (eof($first_fh)) { + last; + } + } + + foreach my $this_fh (@fhs) { + close($this_fh); + } + close(OUT); +} + +sub get_all_arrays_for_species { + my ($dbh, $species) = @_; + my $arrays; + + my $sth = $dbh->prepare("SELECT array_id, array_name FROM array WHERE species_name = ?"); + $sth->execute($species); + $arrays = $sth->fetchall_arrayref(); + $sth->finish(); + + return $arrays; +} + +sub get_probe_mapping_id { + my ($dbh, $this_array_id, $assembly_name) = @_; + my $sql = "SELECT probe_mapping_id + FROM probe_mapping_info + JOIN assembly USING (assembly_id) + WHERE array_id = $this_array_id + AND assembly_name = '$assembly_name'"; + my $probe_mapping_id = $dbh->selectrow_array($sql); + return($probe_mapping_id); +} + +sub dump_array_bed_file { + my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_; + my $sql = "SELECT probe_mapping_id + FROM probe_mapping_info + JOIN assembly USING (assembly_id) + WHERE array_id = $this_array_id + AND assembly_name = '$assembly_name'"; + my $probe_mapping_id = $dbh->selectrow_array($sql); + + $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id"; + my $probes = $dbh->selectall_arrayref($sql); + + my $bed_file = "$work_dir/array_${this_array_id}.bed"; + open(BED, ">$bed_file") or die "Cannot open temporary BED file <$bed_file>\n"; + foreach my $this_probe (sort _sort_probes @$probes) { + print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n"; + } + close(BED); + + return $bed_file; +} + +sub _sort_probes { + my $chr_a = $a->[1]; + my $chr_b = $b->[1]; + my $loc_a = $a->[2]; + my $loc_b = $b->[2]; + $chr_a =~ s/chr//; + $chr_b =~ s/chr//; + if ($chr_a eq $chr_b) { + return $loc_a <=> $loc_b; + } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) { + return $chr_a <=> $chr_b; + } elsif ($chr_a =~ /^\d/) { + return -1; + } elsif ($chr_b =~ /^\d/) { + return 1; + } else { + return $chr_a cmp $chr_b; + } +} + +exit(); + + + + + + diff --git a/eForge/eForge.pm b/eForge/eForge.pm index 824262d..7121134 100644 --- a/eForge/eForge.pm +++ b/eForge/eForge.pm @@ -1,26 +1,55 @@ package eForge::eForge; -use 5.010; -use strict; -use warnings FATAL => 'all'; -use Storable; - =head1 NAME -eForge - The great new eForge! +eForge::eForge - Interface with the DB and various other common functions for eForge =head1 VERSION Version 0.01 +=head1 LICENCE AND COPYRIGHT + +Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; version 2 dated June, 1991 or at your option +any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +A copy of the GNU General Public License is available in the source tree; +if not, write to the Free Software Foundation, Inc., +51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +=head1 CONTACT + +Charles Breeze, C<< >> + +Javier Herrero, C<< >> + +=head1 ACKNOWLEDGEMENTS + +This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI + =cut +use 5.010; +use strict; +use warnings FATAL => 'all'; +use Storable; + + my $MAX_SQL_VARIABLES = 999; our $VERSION = '0.01'; our (@ISA, @EXPORT); use Exporter; @ISA = qw(Exporter); -@EXPORT = qw(process_file match process_bits get_bits fetch_rsid fetch_loc get_cells assign bkgrdstat prox_filter); +@EXPORT = qw(get_all_datasets get_all_arrays get_all_proxy_filters process_file match process_bits get_bits get_cells assign bkgrdstat prox_filter); =head1 SYNOPSIS @@ -28,12 +57,13 @@ Provide functional modules for eForge =head1 EXPORT +get_all_datasets +get_all_arrays +get_all_proxy_filters process_file match process_bits get_bits -fetch_rsid -fetch_loc get_cells assign bkgrdstat @@ -67,85 +97,66 @@ sub bkgrdstat{ say $bfh join("\t", $flag, "cpg_island_relationship", @cpg_island_relationship); } + =head2 process_file -Processes various file formats. + Arg[1] : FILEHANDLE $input_fh + Arg[2] : string $format + Arg[3] : DB-connection-handle $dbh + Arg[4] : string $bkgd + Arg[5] : numeric $filter + Returns : arrayref of $probe_ids (string) + Example : my $probe_ids = process_file($fh, "probeid", $dbh, '450k', undef); + Description : Reads the list of probe IDs or locations from the file. If the file contains + locations, these will be translated into probe_ids + Exceptions : =cut sub process_file { - my ($fh, $format, $sth, $filter) = @_; - my @snps; - if ($format =~ /probeid/){ - while (<$fh>){ + my ($fh, $format, $dbh, $bkgd, $filter) = @_; + my $probe_ids = []; + + if ($format =~ /^probe/i) { + while (<$fh>) { next if /^#/; chomp; - my $rs; + my $probe_id; if (defined $filter) { my $pval; - ($rs, $pval) = split /\s+/, $_; + ($probe_id, $pval) = split /\s+/, $_; next unless $pval >= $filter; - } - else{ - ($rs, undef) = split /\s+/, $_; # remove anything that is not supposed to be there :-) - } - my @rsid = split /\:/, $rs; - my $rsid = pop @rsid; # take the last one for want of a better idea. - push @snps, $rsid; - } - } - elsif ($format =~ /ian/){ - while (<$fh>){ - my ($chr, $beg, $end, $rsid, $p, $pval) = split "\t", $_; - if (defined $filter) { - next unless $pval >= $filter; - } - my @rsid = split /\:/, $rsid; # to deal with multiple rsids - $rsid = pop @rsid; # take the last one for want of a better idea. Can't take all as they are the same thing. - push @snps, $rsid; - } - } - elsif ($format =~ /vcf/){ - while (<$fh>){ - next if /^#/; - my ($chr, $beg, $rsid) = split "\t", $_; + } else { + ($probe_id, undef) = split /\s+/, $_; # remove anything that is not supposed to be there :-) + } + push @$probe_ids, $probe_id; + } + + } elsif ($format =~ /^bed/i) { + my $locations = []; + while (<$fh>) { + next if /^track/; + chomp; + my ($chr, $from, $to) = split "\t", $_; + next if (!defined($to)); unless ($chr =~ /^chr/){ $chr = "chr". $chr; - } - if ($rsid =~ /^cg\d+/){ - push @snps, $rsid; - } - else { - my $loc = "$chr:$beg-$beg"; - #get the rsid from the db - $rsid = fetch_rsid($loc, $sth); - push @snps, $rsid if defined $rsid; - } - } - } - elsif ($format =~ /bed|tabix/){ - while (<$fh>){ - my $loc; - if ($format =~/bed/){ - next if /^track/; - chomp; - my ($chr, $beg, $end) = split "\t", $_; - unless ($chr =~ /^chr/){ - $chr = "chr". $chr; - } - $loc = "$chr:$beg-$beg"; - } - elsif ($format =~ /tabix/){ - chomp; - $loc = $_; - } - #get the $rsid from the db - my $rsid = fetch_rsid($loc, $sth); - push @snps, $rsid if defined $rsid; - } - } - return @snps; - } + } + push(@$locations, [$chr, $from]); + } + $probe_ids = fetch_all_probe_ids($dbh, $bkgd, $locations); + + } elsif ($format =~ /^tabix/i) { + my $locations = []; + while (<$fh>) { + chomp; + my ($chr, $from, $to) = $_ =~ /(.+)\:(\d+)\-(\d+)/; + push(@$locations, [$chr, $from]); + } + $probe_ids = fetch_all_probe_ids($dbh, $bkgd, $locations); + } + return $probe_ids; +} =head2 match @@ -240,51 +251,154 @@ sub match{ =head2 process_bits -Processes bitstrings to get a count of overlaps for each cell type. + Arg[1] : arrayref of arrays $rows ($probe_id, $sum, $bit_string, $feature, $CGI_context) + Arg[2] : arrayref of strings $cells (shortname for the cells in the dataset) + Arg[3] : string $dataset + Returns : hashref $stats + Example : my $result = process_bits($rows, $cells, 'erc'); + Description : Returns a reference to a complex hash with stats from the rows. These are split + into 'MVPS' and 'CELLS'. The former contains 'SUM' and 'PARAMS' for each probe ID + while the latter contains 'COUNT' and 'MVPS' for each cell. + Exceptions : Dies if the number of cells does not match the length of the bit string. =cut -sub process_bits{ +sub process_bits { my ($rows, $cells, $data) = @_; my %test; my @test_cells; my @indexes = 0..(@$cells-1); foreach my $row (@{$rows}){ - my ($location, $probeid, $sum, $bit_string, $feature, $cpg_island_relationship); - if ($data eq "erc"){ - ($location, $probeid, undef, undef, $bit_string, $sum, undef, undef, undef, undef, $feature, $cpg_island_relationship) = @$row; - } - elsif ($data eq "encode"){ - ($location, $probeid, $bit_string, $sum, undef, undef, undef, undef, undef, undef, $feature, $cpg_island_relationship) = @$row; - } - elsif ($data eq "blueprint"){ - ($location, $probeid, undef, undef, undef, undef, $bit_string, $sum, undef, undef, $feature, $cpg_island_relationship) = @$row; - } - elsif ($data eq "erc2"){ - ($location, $probeid, undef, undef, undef, undef, undef, undef, $bit_string, $sum, $feature, $cpg_island_relationship) = @$row; - } + my ($probeid, $sum, $bit_string, $feature, $cpg_island_relationship) = @$row; $test{'MVPS'}{$probeid}{'SUM'} = $sum; $test{'MVPS'}{$probeid}{'PARAMS'} = join("\t", $feature, $cpg_island_relationship); - die if (scalar(@$cells) ne length($bit_string)); + die "For $data, found ".scalar(@$cells)." cells for ".length($bit_string)." bits\n" if (scalar(@$cells) ne length($bit_string)); foreach my $index (@indexes) { ## $bit_string is a string made of 0s and 1s. If it is a 1 for this position, count and push if (substr($bit_string, $index, 1)) { $test_cells[$index][0]++; push @{$test_cells[$index][1]}, $probeid; } - } - } + } + } my $index = 0; foreach my $cell (@$cells){ $test{'CELLS'}{$cell}{'COUNT'} = $test_cells[$index][0] if ($test_cells[$index][0]); $test{'CELLS'}{$cell}{'MVPS'} = $test_cells[$index][1] if ($test_cells[$index][1]); $index++; - } + } return \%test; - } +} + + +=head2 get_all_datasets + + Arg[1] : DB-handle $dbh + Arg[2] : (optional) string $species_name + Returns : arrayref of hashes (tag/name) + Example : my $all_datasets = get_all_dataset($dbh); + Description : Returns the list of all datasets in the DB. It returns an arrayref of hashes. Each + hash has two keys: 'tag' (string ID of the dataset) and 'name' (full name). You + can limit the dataset to the ones available for a given species. + Exceptions : + +=cut + +sub get_all_datasets { + my ($dbh, $species_name) = @_; + my $datasets; + + my $sql = "SELECT dataset_tag, dataset_name FROM dataset ORDER BY dataset_id"; + my @bind_params = (); + if ($species_name) { + $sql .= " WHERE species_name = ?"; + push(@bind_params, $species_name); + } + my ($tag, $name); + my $sth = $dbh->prepare($sql); + $sth->execute(@bind_params); + $sth->bind_columns(\$tag, \$name); + while ($sth->fetch) { + push(@$datasets, {tag => $tag, name => $name}); + } + + return($datasets); +} +=head2 get_all_arrays + + Arg[1] : DB-handle $dbh + Arg[2] : (optional) string $species_name + Returns : arrayref of hashes (tag/name) + Example : my $all_arrays = get_all_arrays($dbh); + Description : Returns the list of all arrays in the DB. It returns an arrayref of hashes. Each + hash has two keys: 'tag' (string ID of the array) and 'name' (full name). You + can limit the arrays to the ones available for a given species. + Exceptions : + +=cut + +sub get_all_arrays { + my ($dbh, $species_name) = @_; + my $arrays; + + my $sql = "SELECT array_tag, array_name FROM array order by array_id"; + my @bind_params = (); + if ($species_name) { + $sql .= " WHERE species_name = ?"; + push(@bind_params, $species_name); + } + my ($tag, $name); + my $sth = $dbh->prepare($sql); + $sth->execute(); + $sth->bind_columns(\$tag, \$name); + while ($sth->fetch) { + push(@$arrays, {tag => $tag, name => $name}); + } + + return($arrays); +} + + +=head2 get_all_proxy_filters + + Arg[1] : DB-handle $dbh + Arg[2] : (optional) string $bkgd + Returns : hashref of proxy-filters (string) + Example : my $proxy_filters = get_all_proxy_filters($dbh, '450k'); + Description : Returns the list of proxy filters available in the DB. It returns a hashref whose + keys are the bkgd names (i.e. array tags) and values are the name of the proxy + filter. At the moment the schema supports just one proxy filter per array. + If you provide a $bkgd, the result will be limited to that array. Note that you + will still get a hashref with exactly the same structure. Only the content will + be limited. + Exceptions : + +=cut + +sub get_all_proxy_filters { + my ($dbh, $array_tag) = @_; + my $proxy_filters; + + my $sql = "SELECT array_tag, description FROM proxy_filter_info JOIN array USING (array_id)"; + my @bind_params = (); + if ($array_tag) { + $sql .= " WHERE array_tag = ?"; + push(@bind_params, $array_tag); + } + my ($this_array_tag, $description); + my $sth = $dbh->prepare($sql); + $sth->execute(); + $sth->bind_columns(\$this_array_tag, \$description); + while ($sth->fetch) { + $proxy_filters->{$this_array_tag} = $description; + } + + return($proxy_filters); +} + =head2 get_bits Get the bitstrings for an array of mvps from the sqlite db @@ -292,8 +406,7 @@ Get the bitstrings for an array of mvps from the sqlite db =cut sub get_bits{ - - my ($mvps, $dbh) = @_; + my ($dbh, $dataset_tag, $array_tag, $mvps) = @_; my @results; for (my $loop = 0; $loop * $MAX_SQL_VARIABLES < @$mvps; $loop++) { @@ -301,42 +414,60 @@ sub get_bits{ my $end = ($loop + 1) * $MAX_SQL_VARIABLES - 1; $end = @$mvps -1 if ($end >= @$mvps); - my $sql = "SELECT * FROM bits WHERE probeid IN (?". (",?" x ($end - $start)).")"; + my $sql = "SELECT probe_id, sum, bit, gene_group, cgi_group + FROM probe_annotation + JOIN probe_bitstring USING (array_id, probe_id) + JOIN dataset USING (dataset_id) + JOIN array ON (array.array_id = probe_annotation.array_id) + WHERE array_tag = ? and dataset_tag = ? + AND probe_id IN (?". (",?" x ($end - $start)).")"; my $sth = $dbh->prepare_cached($sql); #get the blocks form the ld table - $sth->execute(@$mvps[$start..$end]); + $sth->execute($array_tag, $dataset_tag, @$mvps[$start..$end]); while (my $row = $sth->fetchrow_arrayref()) { - push @results, [@$row]; + push @results, [@$row]; } $sth->finish(); - } + } return \@results;# return the bitstring line from the database - } +} + -=head2 fetch_rsid +=head2 fetch_all_probe_ids -gets the rsid for a SNP where a location is given. + Arg[1] : DB-handle $dbh + Arg[2] : string $bkgd + Arg[3] : arrayref of locations [$chr, $pos] + Returns : arrayref of probe IDs (string) + Description : Given a list of chromosome names and location pairs, the method fetches the name + of the probe ID for that location. To do this successfully, this method requires + to know the background (i.e. array) you want to translate the locations to. + Exceptions : =cut -sub fetch_rsid{ +sub fetch_all_probe_ids { #gets the rsid for a SNP where a location is given - my ($loc, $sth) = @_; - $sth->execute($loc); - my $result = $sth->fetchall_arrayref(); - my $rsid; - foreach my $row (@{$result}){ - $rsid = $$row[0]; - } + my ($dbh, $bkgd, $locations) = @_; + + my $sth = $dbh->prepare("SELECT probe_id + FROM probe_mapping + WHERE chr_name = ? AND position = ?"); + my $probe_ids = []; + + foreach my $this_loc (@$locations) { + my ($chr, $pos) = @$this_loc; + $sth->execute($chr, $pos); + my $result = $sth->fetchall_arrayref(); + my $probe_id; + foreach my $row (@{$result}) { + push(@$probe_ids, $$row[0]); + } + } $sth->finish(); - if (defined $rsid &&$rsid =~ /^cg\d+/){ - return $rsid; - } - else{ - return "no PROBEID match for $loc"; - } - } + return $probe_ids; +} =head2 prox_filter @@ -357,7 +488,7 @@ sub prox_filter{ my $end = ($loop + 1) * $MAX_SQL_VARIABLES - 1; $end = @$mvps -1 if ($end >= @$mvps); - my $sql = "SELECT probeid,proxy_probes FROM proxy_filter WHERE probeid IN (?". (",?" x ($end - $start)).")"; + my $sql = "SELECT probe_id,proxy_probes FROM proxy_filter WHERE probe_id IN (?". (",?" x ($end - $start)).")"; my $sth = $dbh->prepare($sql); #get the blocks form the ld table $sth->execute(@$mvps[$start..$end]); my $result = $sth->fetchall_arrayref(); @@ -379,118 +510,33 @@ sub prox_filter{ return (\%prox_excluded, @mvps_filtered); } - =head2 get_cells Read the correct cell list based on data (erc, erc2, blueprint or encode). Also gets the tissue names for the cells. =cut -sub get_cells{ - # read the correct cell list based on data (erc, erc2, blueprint or encode). Also gets the tissue names for the cells. - my ($data, $dbh) = @_; - - my $table = "cells_".$data; - - # Check that the table exists in the DB (note, some magic here that might be SQLite-specific) - my @tables = grep {/^cells_/} map {$_ =~ s/"//g; $_ =~ s/^main\.//; $_} $dbh->tables(); - if (!grep {/$table/} @tables) { - die "The database does not contain information for the data background provided.\n"; +sub get_cells { + my ($dataset_tag, $dbh) = @_; + my $samples; + + my $sth = $dbh->prepare("SELECT shortcell, tissue, datatype, file, acc FROM dataset JOIN sample USING (dataset_id) WHERE dataset_tag = ? ORDER BY sample_order"); + $sth->execute($dataset_tag); + my ($shortcell, $tissue, $datatype, $file, $acc); + $sth->bind_columns(\$shortcell, \$tissue, \$datatype, \$file, \$acc); + my ($cells, $tissues); + while ($sth->fetch) { + $shortcell = "$shortcell|$file"; # Sometimes the same cell is used twice, with a differnt file so need to record separately (e.g. WI-38). + push @$cells, $shortcell; + $$tissues{$shortcell}{'tissue'} = $tissue; # this is the hash that is used to connect cells and tissues and ultimately provide the sorting order + $$tissues{$shortcell}{'datatype'} = $datatype; + $$tissues{$shortcell}{'file'} = $file; + $$tissues{$shortcell}{'acc'} = $acc; } +# use Data::Dumper; +# print Dumper %$tissues; - my $sth = $dbh->prepare("SELECT shortcell,tissue,file,acc FROM $table"); - $sth->execute(); - my $ver = $sth->fetchall_arrayref(); - $sth->finish(); - my ($cells, $tissues, $acc); - foreach my $row (@$ver){ - my $cell = shift @$row; - my $tissue = shift @$row; - my $file = shift @$row; - my $acc = shift @$row; - $cell = "$cell|$file"; # Sometimes the same cell is used twice, with a differnt file so need to record separately (e.g. WI-38). - push @$cells, $cell; - $$tissues{$cell}{'tissue'} = $tissue; # this is the hash that is used to connect cells and tissues and ultimately provide the sorting order - $$tissues{$cell}{'file'} = $file; - $$tissues{$cell}{'acc'} = $acc; - } - #print Dumper %$tissues; return ($cells, $tissues); # return - } - -=head2 assign - -Assign any maf, gc, tss values to the percentile bins - -=cut - -#sub assign{ -# #sub routine to assign any maf, gc, tss values to the percentile bins -# my ($gc, $tss, $maf, $params) = @_; -# my ($i, $j, $k); -# my $n = 1; -# foreach my $pc (@{$$params{'gc'}}){ -# if ($gc <= $pc) { -# $i = $n; -# } -# else{ -# $n++; -# } -# } -# $n=1; -# foreach my $pc (@{$$params{'tss'}}){ -# if ($tss <= $pc) { -# $j = $n; -# } -# else{ -# $n++; -# } -# } -# $n=1; -# foreach my $pc (@{$$params{'maf'}}){ -# if ($maf <= $pc) { -# $k = $n; -# } -# else{ -# $n++; -# } -# } -# return ($i, $j, $k); -# } - -=head1 AUTHOR - -Charles Breeze, C<< >> - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc eForge - - -=head1 ACKNOWLEDGEMENTS - - -=head1 LICENSE AND COPYRIGHT - -Copyright 2015 Charles Breeze. - -This program is free software; you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation; version 2 dated June, 1991 or at your option -any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -A copy of the GNU General Public License is available in the source tree; -if not, write to the Free Software Foundation, Inc., -51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - - -=cut +} 1; diff --git a/eForge/ePlot.pm b/eForge/ePlot.pm index b95aa1f..602ff65 100644 --- a/eForge/ePlot.pm +++ b/eForge/ePlot.pm @@ -1,10 +1,5 @@ package eForge::ePlot; -use 5.010; -use strict; -use warnings FATAL => 'all'; -use Sort::Naturally; - =head1 NAME eForge::ePlot - Plotting utilities for eForge @@ -13,8 +8,41 @@ eForge::ePlot - Plotting utilities for eForge Version 0.01 +=head1 LICENCE AND COPYRIGHT + +Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; version 2 dated June, 1991 or at your option +any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +A copy of the GNU General Public License is available in the source tree; +if not, write to the Free Software Foundation, Inc., +51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +=head1 CONTACT + +Charles Breeze, C<< >> + +Javier Herrero, C<< >> + +=head1 ACKNOWLEDGEMENTS + +This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI + =cut +use 5.010; +use strict; +use warnings FATAL => 'all'; +use Sort::Naturally; + our $VERSION = '0.01'; our (@ISA, @EXPORT, @EXPORT_OK); @@ -43,7 +71,7 @@ This is the original code using standard R plot to generate a static pdf. sub Chart{ print "Making static chart.\n"; - my ($filename, $lab, $resultsdir, $tissues, $cells, $label, $t1, $t2, $data) = @_; + my ($filename, $lab, $resultsdir, $tissues, $cells, $label, $t_marginal, $t_strict, $data) = @_; my $Rdir = $resultsdir; my $chart = "$lab.chart.pdf"; my $rfile = "$Rdir/$lab.chart.R"; @@ -52,17 +80,17 @@ sub Chart{ open my $rfh, ">", $rfile; -#results\$Class<-cut(results\$Pvalue, breaks =c(min(results\$Pvalue), $t1, $t2, max(results\$Pvalue)), labels=FALSE, include.lowest=TRUE) # 99 and 95% CIs 1, 2, 3 -$t1 = sprintf("%.2f", $t1); -$t2 = sprintf("%.2f", $t2); +#results\$Class<-cut(results\$Pvalue, breaks =c(min(results\$Pvalue), $t_marginal, $t_strict, max(results\$Pvalue)), labels=FALSE, include.lowest=TRUE) # 99 and 95% CIs 1, 2, 3 +$t_marginal = sprintf("%.2f", $t_marginal); +$t_strict = sprintf("%.2f", $t_strict); print $rfh "setwd('$Rdir') results<-read.table('$filename', header=TRUE,sep='\\t') -# Class splits the data into non-significant, marginally significant and significant according to $t1 and $t2 (in -log10 scale) -results\$Class <- cut(results\$Pvalue, breaks =c(0, $t2, $t1, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE) +# Class splits the data into non-significant, marginally significant and significant according to $t_marginal and $t_strict (in -log10 scale) +results\$Class <- cut(results\$Pvalue, breaks =c(0, $t_strict, $t_marginal, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE) # Class splits the data into non-significant, marginally significant and significant according to q-value (B-Y FDR adjusted) -results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t2, $t1, 1), labels=FALSE, include.lowest=TRUE) +results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t_strict, $t_marginal, 1), labels=FALSE, include.lowest=TRUE) # Re-order the entries according to tissue first and then cell type/line tissue.cell.order <- unique(results[, c('Tissue', 'Cell')]) @@ -103,11 +131,11 @@ mtext(2, text='-log10 binomial p-value', line=2, cex=1.4) # Add legend (internal color first) palette(c('white', '$msig', '$sig')) -legend('topleft', pch=19, legend=c('q < 0.01', 'q < 0.05', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='white', title='FDR q-value', text.col='white', bg='white') +legend('topleft', pch=19, legend=c('q < $t_strict', 'q < $t_marginal', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='white', title='FDR q-value', text.col='white', bg='white') # Add contour to the points in the legend palette(c('$ns', '$msig', 'black')) -legend('topleft', pch=1, legend=c('q < 0.01', 'q < 0.05', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='darkgrey', title='FDR q-value') +legend('topleft', pch=1, legend=c('q < $t_strict', 'q < $t_marginal', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='darkgrey', title='FDR q-value') palette('default') dev.off() @@ -125,7 +153,7 @@ Make dimple interactive chart. =cut sub dChart{ - my ($filename, $lab, $resultsdir, $data, $label, $t1, $t2, $web) = @_; + my ($filename, $lab, $resultsdir, $data, $label, $t_marginal, $t_strict, $web) = @_; print "Making dChart.\n"; my $chart = "$lab.dchart.html"; @@ -135,11 +163,22 @@ sub dChart{ print $rcfh "setwd(\"$Rdir\") results<-read.table(\"$filename\", header = TRUE, sep=\"\\t\") -# Class splits the data into non-significant, marginally significant and significant according to $t1 and $t2 (in -log10 scale) -results\$Class <- cut(results\$Pvalue, breaks =c(0, $t2, $t1, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE) +# Class splits the data into non-significant, marginally significant and significant according to $t_marginal and $t_strict (in -log10 scale) +results\$Class <- cut(results\$Pvalue, breaks =c(0, $t_strict, $t_marginal, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE) # Class splits the data into non-significant, marginally significant and significant according to q-value (B-Y FDR adjusted) -results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t2, $t1, 1), labels=FALSE, include.lowest=TRUE) +results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t_strict, $t_marginal, 1), labels=FALSE, include.lowest=TRUE) +color.axis.palette = c(); +if (length(which(results\$Class2 == 1)) > 0 ) { + color.axis.palette = c('red'); +} +if (length(which(results\$Class2 == 2)) > 0 ) { + color.axis.palette = c(color.axis.palette, '#FF82ab'); +} +color.axis.palette = c(color.axis.palette, 'lightblue'); +if (length(color.axis.palette) < 2) { + color.axis.palette = c(color.axis.palette, 'lightblue'); # Add it twice to force the color if only non-significant values +} results\$log10pvalue <- -log10(results\$Pvalue) @@ -167,7 +206,7 @@ bounds.width=dplot.width - bounds.x - 20 d1 <- dPlot( y = 'log10pvalue', x = c('TissueCell'), - groups = c('TissueCell', 'Accession', 'Pvalue', 'Qvalue', 'Probe'), + groups = c('TissueCell', 'Accession', 'Pvalue', 'Qvalue', 'Datatype', 'Probe'), data = results, type = 'bubble', width = dplot.width, @@ -186,7 +225,7 @@ d1\$yAxis( type = 'addMeasureAxis' ) d1\$colorAxis( type = 'addColorAxis', colorSeries = 'Class2', - palette = c('red', 'pink', 'lightblue')) + palette = color.axis.palette) # Builds a JS string to add labels for tissues labels.string = paste(paste0(\" @@ -298,7 +337,7 @@ sub table{ open my $rcfh, ">", $rfile; print $rcfh "setwd('$Rdir') results <- read.table('$filename', header = TRUE, sep='\\t') -results <- subset(results, T, select = c('Cell', 'Tissue', 'Accession', 'Pvalue', 'Qvalue', 'Probe')) +results <- subset(results, T, select = c('Cell', 'Tissue', 'Datatype', 'Accession', 'Pvalue', 'Qvalue', 'Probe')) require(rCharts) dt <- dTable( results, @@ -326,49 +365,4 @@ dt\$save('$chart', cdn = F)\n"; } } - -=head1 AUTHOR - -Charles Breeze, C<< >> - -=head1 BUGS - -Please report any bugs or feature requests to C, or through -the web interface at L. I will be notified, and then you'll -automatically be notified of progress on your bug as I make changes. - - - - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc eForge::ePlot - - -=head1 ACKNOWLEDGEMENTS - - -=head1 LICENSE AND COPYRIGHT - -Copyright 2015 Charles Breeze. - -This program is free software; you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation; version 2 dated June, 1991 or at your option -any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -A copy of the GNU General Public License is available in the source tree; -if not, write to the Free Software Foundation, Inc., -51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - - -=cut - -1; # End of ePlot +1; diff --git a/eForge/eStats.pm b/eForge/eStats.pm index 14421ce..ca6334d 100644 --- a/eForge/eStats.pm +++ b/eForge/eStats.pm @@ -1,19 +1,48 @@ package eForge::eStats; -use 5.010; -use strict; -use warnings FATAL => 'all'; - =head1 NAME -eStats - Stats for use in eForge +eForge::eStats - Stats for use in eForge =head1 VERSION Version 0.01 +=head1 LICENCE AND COPYRIGHT + +Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; version 2 dated June, 1991 or at your option +any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +A copy of the GNU General Public License is available in the source tree; +if not, write to the Free Software Foundation, Inc., +51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +=head1 CONTACT + +Charles Breeze, C<< >> + +Javier Herrero, C<< >> + +=head1 ACKNOWLEDGEMENTS + +This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI + =cut + +use 5.010; +use strict; +use warnings FATAL => 'all'; + our $VERSION = '0.01'; our (@ISA, @EXPORT); @@ -174,51 +203,4 @@ sub fdr{ } } - - - - -=head1 AUTHOR - -Charles Breeze, C<< >> - -=head1 BUGS -#not yet implemented below, it refers to eForge but it is not yet implemented (for cpan) even for Forge -Please report any bugs or feature requests to C, or through -the web interface at L. I will be notified, and then you'll -automatically be notified of progress on your bug as I make changes. - - - - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc Forge::eStats - - - -=head1 ACKNOWLEDGEMENTS - - -=head1 LICENSE AND COPYRIGHT - -eForge::eStats.pm - -Copyright (C) 2015 EMBL - European Bioinformatics Institute and University College London - -This program is free software: you can redistribute it and/or modify it under the terms of -the GNU General Public License as published by the Free Software Foundation, either version 3 -of the License, or (at your option) any later version. This program is distributed in the hope -that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY -or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Neither -the institution name nor the name eforge.pl can be used to endorse or promote products derived from -this software without prior written permission. For written permission, please contact -c.breeze@ucl.ac.uk . Products derived from this software may not be called eforge.pl nor may eforge.pl -appear in their names without prior written permission of the developers. You should have received -a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. - -=cut - -1; # End of eStats +1; diff --git a/eforge.pl b/eforge.pl index 9482acb..59914f1 100644 --- a/eforge.pl +++ b/eforge.pl @@ -37,6 +37,8 @@ =head1 OPTIONS Dataset to analyse. Either ENCODE data ('encode'), unconsolidated Roadmap Epigenome data ('erc'), consolidated Roadmap Epigenome data ('erc2'), or Blueprint data ('blueprint'). erc by default. +Use -data ? to get a list of available datasets on your local install. + =item B Use peaks instead of hotspots. Peaks are more stringent DNase1 peaks calls representing DNase hypersensitive sites, @@ -48,6 +50,8 @@ =head1 OPTIONS For the time being, it is suficient for MVPs to be on the 450k array. Probes within 1kb of each other will undergo filtering. +Use -bkgd ? to get a list of available backgrounds on your local install. + =item B