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| Original file line number | Diff line number | Diff line change |
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| @@ -1,7 +1,7 @@ | ||
| "Sample Name" "Protocol REF" "Factor Value[tissue,http://purl.obolibrary.org/obo/UBERON_0000479,UBERON]" "Term Source REF" "Term Accession Number" "Extract Name" "Parameter Value[library layout]" "Parameter Value[sequencing instrument]" "Assay Name" "Raw Data File" "Derived Data File" | ||
| "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494" "nucleic acid extraction" "inflorescence" "BTO" "" "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494.Extract-1" "SINGLE" "" "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494.Extract-1.LE-1.ASSAY-1" "SRR9041387" "" | ||
| "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494" "nucleic acid extraction" "inflorescence" "BTO" "" "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494.Extract-2" "SINGLE" "" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619494.Extract-2.LE-1.ASSAY-1" "SRR9041386" "" | ||
| "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494" "nucleic acid extraction" "inflorescence" "BTO" "" "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494.Extract-3" "SINGLE" "" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619494.Extract-3.LE-1.ASSAY-1" "SRR9041388" "" | ||
| "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494" "nucleic acid extraction" "inflorescence" "BTO" "http://purl.obolibrary.org/obo/BTO_0000628" "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494.Extract-1" "SINGLE" "" "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494.Extract-1.LE-1.ASSAY-1" "SRR9041387" "" | ||
| "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494" "nucleic acid extraction" "inflorescence" "BTO" "http://purl.obolibrary.org/obo/BTO_0000628" "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494.Extract-2" "SINGLE" "" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619494.Extract-2.LE-1.ASSAY-1" "SRR9041386" "" | ||
| "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494" "nucleic acid extraction" "inflorescence" "BTO" "http://purl.obolibrary.org/obo/BTO_0000628" "CBGP UPM-INIA.Group-1.Subject-1.sSAMN11619494.Extract-3" "SINGLE" "" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619494.Extract-3.LE-1.ASSAY-1" "SRR9041388" "" | ||
| "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493" "nucleic acid extraction" "leaf" "BTO" "http://purl.obolibrary.org/obo/BTO_0000713" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493.Extract-1" "SINGLE" "" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493.Extract-1.LE-1.ASSAY-1" "SRR9041389" "" | ||
| "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493" "nucleic acid extraction" "leaf" "BTO" "http://purl.obolibrary.org/obo/BTO_0000713" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493.Extract-2" "SINGLE" "" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493.Extract-2.LE-1.ASSAY-1" "SRR9041397" "" | ||
| "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493" "nucleic acid extraction" "leaf" "BTO" "http://purl.obolibrary.org/obo/BTO_0000713" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493.Extract-3" "SINGLE" "" "CBGP UPM-INIA.Group-2.Subject-1.sSAMN11619493.Extract-3.LE-1.ASSAY-1" "SRR9041396" "" |
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| ONTOLOGY SOURCE REFERENCE | ||
| Term Source Name BTO UBERON CHMO OBI | ||
| Term Source File http://data.bioontology.org/ontologies/BTO http://data.bioontology.org/ontologies/UBERON http://data.bioontology.org/ontologies/CHMO http://data.bioontology.org/ontologies/OBI | ||
| Term Source Version 33 269 18 38 | ||
| Term Source Description BRENDA Tissue and Enzyme Source Ontology Uber Anatomy Ontology Chemical Methods Ontology Ontology for Biomedical Investigations | ||
| INVESTIGATION | ||
| Investigation Identifier 1561627179431 | ||
| Investigation Title Genome-wide analysis of H3K27me3 in Brassica rapa | ||
| Investigation Description Study of the genome-wide levels of H3K27me3 in leaves and inflorescences of B. rapa R-o-18, an oilseed variety, and its correlation with transcriptional activity of the marked genes. | ||
| Investigation Submission Date | ||
| Investigation Public Release Date | ||
| Comment[Created With Configuration] /tmp/Configurations/1561623423279/isaconfig-default_v2015-07-02 | ||
| Comment[Last Opened With Configuration] isaconfig-markchip | ||
| INVESTIGATION PUBLICATIONS | ||
| Investigation PubMed ID | ||
| Investigation Publication DOI | ||
| Investigation Publication Author List | ||
| Investigation Publication Title | ||
| Investigation Publication Status | ||
| Investigation Publication Status Term Accession Number | ||
| Investigation Publication Status Term Source REF | ||
| INVESTIGATION CONTACTS | ||
| Investigation Person Last Name Crevillen Wilkinson Miriam Laura Paxti David | ||
| Investigation Person First Name Pedro Mark Payá-Milans Poza-Viejo San Martín-Uriz Lara-Astiaso | ||
| Investigation Person Mid Initials D | ||
| Investigation Person Email crevillen.pedro@inia.es mark.wilkinson@upm.es | ||
| Investigation Person Phone | ||
| Investigation Person Fax | ||
| Investigation Person Address Centro de Biotecnología y Genómica de Plantas UPM – INIA Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo, Autopista M-40, Km 38 - 28223 Pozuelo de Alarcón (Madrid) Centro de Biotecnología y Genómica de Plantas UPM – INIA Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo, Autopista M-40, Km 38 - 28223 Pozuelo de Alarcón (Madrid) Centro de Biotecnología y Genómica de Plantas UPM – INIA Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo, Autopista M-40, Km 38 - 28223 Pozuelo de Alarcón (Madrid) Centro de Biotecnología y Genómica de Plantas UPM – INIA Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo, Autopista M-40, Km 38 - 28223 Pozuelo de Alarcón (Madrid) San Martín-Uriz Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain | ||
| Investigation Person Affiliation INIA UPM UPM INIA | ||
| Investigation Person Roles principal investigator role sub-investigator role sub-investigator role sub-investigator role sub-investigator role sub-investigator role | ||
| Investigation Person Roles Term Accession Number http://purl.obolibrary.org/obo/OBI_0000103 | ||
| Investigation Person Roles Term Source REF OBI | ||
| Comment[Investigation Person REF] | ||
| STUDY | ||
| Study Identifier s_PC-BrasH3-S1 | ||
| Study Title Chip-Seq of H3K27me3 sites in Brassica leaves versus inflorescences | ||
| Study Description ChIP experiments were performed using B. rapa R-o-18 wild-type primary leaves collected 14 days after germination. ChIP-seq sequencing libraries were prepared using NEBNext Ultra DNA Library Prep kit (New England BioLabs 7370) starting from 4 ng of immunoprecipitated DNA. One inflorescence and two leaves ChIP-seq biological replicates were sequenced at 2x125 bp paired-end reads in an Illumina HiSeq 2500 platform using the SBS v4 kit (Illumina) | ||
| Comment[Study Grant Number] BIO2015-68031-R RYC-2013-14689 BES-2016-078939 SEV-2016-0672 (2017-2021) | ||
| Comment[Study Funding Agency] Ministerio de Economia y Competitividad (MINECO/FEDER, EU) Ministerio de Economia y Competitividad (MINECO/FEDER, EU) Ministerio de Economia y Competitividad (MINECO/FEDER, EU) Severo Ochoa Programme for Centres of Excellence in R&D (Agencia Estatal de Investigación of Spain) | ||
| Study Submission Date | ||
| Study Public Release Date | ||
| Study File Name s_s_PC-BrasH3-S1.csv | ||
| STUDY DESIGN DESCRIPTORS | ||
| Study Design Type | ||
| Study Design Type Term Accession Number | ||
| Study Design Type Term Source REF | ||
| STUDY PUBLICATIONS | ||
| Study PubMed ID | ||
| Study Publication DOI | ||
| Study Publication Author List | ||
| Study Publication Title | ||
| Study Publication Status | ||
| Study Publication Status Term Accession Number | ||
| Study Publication Status Term Source REF | ||
| STUDY FACTORS | ||
| Study Factor Name UBERON:tissue | ||
| Study Factor Type tissue | ||
| Study Factor Type Term Accession Number http://purl.obolibrary.org/obo/UBERON_0000479 | ||
| Study Factor Type Term Source REF UBERON | ||
| STUDY ASSAYS | ||
| Study Assay File Name a_chipseq_assay.csv | ||
| Study Assay Measurement Type ChIP-Seq Profiling | ||
| Study Assay Measurement Type Term Accession Number http://edamontology.org/topic_3169 | ||
| Study Assay Measurement Type Term Source REF | ||
| Study Assay Technology Type DNA sequencing | ||
| Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 | ||
| Study Assay Technology Type Term Source REF | ||
| Study Assay Technology Platform | ||
| STUDY PROTOCOLS | ||
| Study Protocol Name sample collection chromatin immunoprecipitation | ||
| Study Protocol Type sample collection chromatin immunoprecipitation | ||
| Study Protocol Type Term Accession Number http://purl.obolibrary.org/obo/CHMO_0001694 | ||
| Study Protocol Type Term Source REF CHMO | ||
| Study Protocol Description | ||
| Study Protocol URI https://dx.doi.org/10.17504/protocols.io.444gyyw | ||
| Study Protocol Version | ||
| Study Protocol Parameters Name | ||
| Study Protocol Parameters Name Term Accession Number | ||
| Study Protocol Parameters Name Term Source REF | ||
| Study Protocol Components Name | ||
| Study Protocol Components Type | ||
| Study Protocol Components Type Term Accession Number | ||
| Study Protocol Components Type Term Source REF | ||
| STUDY CONTACTS | ||
| Study Person Last Name Crevillen | ||
| Study Person First Name Pedro | ||
| Study Person Mid Initials | ||
| Study Person Email crevillen.pedro@inia.es | ||
| Study Person Phone | ||
| Study Person Fax | ||
| Study Person Address Centro de Biotecnología y Genómica de Plantas UPM – INIA Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo, Autopista M-40, Km 38 - 28223 Pozuelo de Alarcón (Madrid) | ||
| Study Person Affiliation INIA | ||
| Study Person Roles principal investigator role | ||
| Study Person Roles Term Accession Number http://purl.obolibrary.org/obo/OBI_0000103 | ||
| Study Person Roles Term Source REF OBI | ||
| Comment[Study Person REF] | ||
| STUDY | ||
| Study Identifier s_PC-BrasRNAS-S1 | ||
| Study Title RNASeq of gene expression in Brassica leaves versus inflorescences | ||
| Study Description Total RNA was extracted from plant tissues using EZNA Plant RNA Kit (Omega Bio-tek). Complementary DNA (cDNA) was prepared by reverse transcription of 1 µg of total RNA using “Maxima cDNA Kit with dsDNase”. Quantification was performed by RT-qPCR using the LightCycler 480 and SYBR Green I Master mix (Roche). Gene expression was determined by 2-ΔΔCT method using BraA.TUBULIN (BraA10g026070.3C) [47] as housekeeping gene. | ||
| Comment[Study Grant Number] | ||
| Comment[Study Funding Agency] | ||
| Study Submission Date | ||
| Study Public Release Date | ||
| Study File Name s_s_PC-BrasRNAS-S1.csv | ||
| STUDY DESIGN DESCRIPTORS | ||
| Study Design Type | ||
| Study Design Type Term Accession Number | ||
| Study Design Type Term Source REF | ||
| STUDY PUBLICATIONS | ||
| Study PubMed ID | ||
| Study Publication DOI | ||
| Study Publication Author List | ||
| Study Publication Title | ||
| Study Publication Status | ||
| Study Publication Status Term Accession Number | ||
| Study Publication Status Term Source REF | ||
| STUDY FACTORS | ||
| Study Factor Name UBERON:tissue | ||
| Study Factor Type tissue | ||
| Study Factor Type Term Accession Number http://purl.obolibrary.org/obo/UBERON_0000479 | ||
| Study Factor Type Term Source REF UBERON | ||
| STUDY ASSAYS | ||
| Study Assay File Name a_rnaseq-assay.csv | ||
| Study Assay Measurement Type transcription profiling | ||
| Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000424 | ||
| Study Assay Measurement Type Term Source REF OBI | ||
| Study Assay Technology Type nucleotide sequencing | ||
| Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 | ||
| Study Assay Technology Type Term Source REF OBI | ||
| Study Assay Technology Platform | ||
| STUDY PROTOCOLS | ||
| Study Protocol Name nucleic acid extraction sample collection | ||
| Study Protocol Type nucleic acid extraction sample collection | ||
| Study Protocol Type Term Accession Number | ||
| Study Protocol Type Term Source REF | ||
| Study Protocol Description | ||
| Study Protocol URI | ||
| Study Protocol Version | ||
| Study Protocol Parameters Name | ||
| Study Protocol Parameters Name Term Accession Number | ||
| Study Protocol Parameters Name Term Source REF | ||
| Study Protocol Components Name | ||
| Study Protocol Components Type | ||
| Study Protocol Components Type Term Accession Number | ||
| Study Protocol Components Type Term Source REF | ||
| STUDY CONTACTS | ||
| Study Person Last Name Crevillen | ||
| Study Person First Name Pedro | ||
| Study Person Mid Initials | ||
| Study Person Email crevillen.pedro@inia.es | ||
| Study Person Phone | ||
| Study Person Fax | ||
| Study Person Address Centro de Biotecnología y Genómica de Plantas UPM – INIA Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo, Autopista M-40, Km 38 - 28223 Pozuelo de Alarcón (Madrid) | ||
| Study Person Affiliation INIA | ||
| Study Person Roles principal investigator role | ||
| Study Person Roles Term Accession Number http://purl.obolibrary.org/obo/OBI_0000103 | ||
| Study Person Roles Term Source REF OBI | ||
| Comment[Study Person REF] |
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