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Updating the input files Tests/geo/soft_ex_*.txt; adding soft_ex_affy…

…_chp.txt.
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1 parent ae8f325 commit 0846b5c281368b936e7963eb7dcb641246cfa513 mdehoon committed Jan 21, 2008
Showing with 692 additions and 641 deletions.
  1. +152 −124 Tests/Geo/soft_ex_affy.txt
  2. +68 −0 Tests/Geo/soft_ex_affy_chp.txt
  3. +175 −204 Tests/Geo/soft_ex_dual.txt
  4. +248 −268 Tests/Geo/soft_ex_family.txt
  5. +49 −45 Tests/Geo/soft_ex_platform.txt
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@@ -1,124 +1,152 @@
-^SAMPLE=body wall rep1
-!Sample_title = body wall replicate 1
-!Sample_source_name = body wall
-!Sample_organism = Drosophila melanogaster
-!Sample_characteristics = Wild type, third instar larvae, body wall
-!Sample_molecule = total RNA
-!Sample_extract_protocol = Approximately 200 wild-type (Berlin strain) wandering third-instar larvae were dissected and the wing discs were collected in a drop of PBS on Sylgard (Dow Corning). Discs were cut between the presumptive hinge and the body wall regions using a 30-gauge syringe needle, and fragments were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).
-!Sample_label = biotin
-!Sample_label_protocol = Approximately 8 �g of total RNA was processed to produce biotinylated cRNA targets.
-!Sample_hyb_protocol = standard Affymetrix procedures
-!Sample_scan_protocol = standard Affymetrix procedures
-!Sample_description = Wild type third instar larvae imaginal wing discs
-!Sample_data_processing = Affymetrix Microarray Suite version 5.0
-!Sample_platform_id = GPL72
-#ID_REF =
-#VALUE = MAS5-calculated Signal intensity
-#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
-#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
-!Sample_table_begin
-ID_REF VALUE ABS_CALL DETECTION P-VALUE
-141200_at 36.6 A 0.818657
-141201_at 41.5 A 0.703191
-141202_at 607.3 P 0.000944
-141203_at 1509.1 P 0.000762
-141204_at 837.3 P 0.000613
-141205_at 363.2 P 0.003815
-141206_at 1193.6 P 0.000491
-141207_at 346.6 P 0.001165
-141208_at 257.8 P 0.006575
-141209_at 337.1 P 0.002607
-141210_at 48 A 0.150145
-141211_at 130.7 P 0.005504
-141212_at 1454.3 P 0.000491
-141213_at 21.2 A 0.635055
-141214_at 2372.6 P 0.000491
-141215_at 452.9 P 0.017732
-141216_at 504.1 P 0.006575
-141217_at 716.9 P 0.004591
-141218_at 3248.8 P 0.000491
-141219_at 223.5 P 0.007827
-!Sample_table_end
-^SAMPLE=body wall rep2
-!Sample_title = body wall replicate 2
-!Sample_source_name = body wall
-!Sample_organism = Drosophila melanogaster
-!Sample_characteristics = Wild type, third instar larvae, body wall
-!Sample_molecule = total RNA
-!Sample_extract_protocol = Approximately 200 wild-type (Berlin strain) wandering third-instar larvae were dissected and the wing discs were collected in a drop of PBS on Sylgard (Dow Corning). Discs were cut between the presumptive hinge and the body wall regions using a 30-gauge syringe needle, and fragments were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).
-!Sample_label = biotin
-!Sample_label_protocol = Approximately 8 �g of total RNA was processed to produce biotinylated cRNA targets.
-!Sample_hyb_protocol = standard Affymetrix procedures
-!Sample_scan_protocol = standard Affymetrix procedures
-!Sample_description = Wild type third instar larvae imaginal wing discs
-!Sample_data_processing = Affymetrix Microarray Suite version 5.0
-!Sample_platform_id = GPL72
-#ID_REF =
-#VALUE = MAS5-calculated Signal intensity
-#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
-#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
-!Sample_table_begin
-ID_REF VALUE ABS_CALL DETECTION P-VALUE
-141200_at 70.3 A 0.216313
-141201_at 38 A 0.635055
-141202_at 831.8 P 0.000613
-141203_at 2215.5 P 0.000944
-141204_at 965.6 P 0.000491
-141205_at 383.2 P 0.001432
-141206_at 1195 P 0.000491
-141207_at 413.7 P 0.000613
-141208_at 447.3 P 0.000762
-141209_at 294.4 P 0.004591
-141210_at 81.7 M 0.054711
-141211_at 84.9 P 0.005504
-141212_at 1456.4 P 0.000491
-141213_at 37 A 0.122747
-141214_at 2022 P 0.000491
-141215_at 690.9 P 0.004591
-141216_at 525.1 P 0.000762
-141217_at 643.5 P 0.000613
-141218_at 2570.5 P 0.000491
-141219_at 265.9 P 0.005504
-!Sample_table_end
-^SAMPLE=wing/hinge rep1
-!Sample_title = wing/hinge replicate 1
-!Sample_source_name = wing/hinge
-!Sample_organism = Drosophila melanogaster
-!Sample_characteristics = Wild type, third instar larvae, wing/hinge
-!Sample_molecule = total RNA
-!Sample_extract_protocol = Approximately 200 wild-type (Berlin strain) wandering third-instar larvae were dissected and the wing discs were collected in a drop of PBS on Sylgard (Dow Corning). Discs were cut between the presumptive hinge and the body wall regions using a 30-gauge syringe needle, and fragments were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).
-!Sample_label = biotin
-!Sample_label_protocol = Approximately 8 �g of total RNA was processed to produce biotinylated cRNA targets.
-!Sample_hyb_protocol = standard Affymetrix procedures
-!Sample_scan_protocol = standard Affymetrix procedures
-!Sample_description = Wild type third instar larvae imaginal wing discs
-!Sample_data_processing = Affymetrix Microarray Suite version 5.0
-!Sample_platform_id = GPL72
-#ID_REF =
-#VALUE = MAS5-calculated Signal intensity
-#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
-#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
-!Sample_table_begin
-ID_REF VALUE ABS_CALL DETECTION P-VALUE
-141200_at 20.8 A 0.801637
-141201_at 85.8 A 0.48748
-141202_at 704.8 P 0.000613
-141203_at 1036.6 P 0.000944
-141204_at 700.3 P 0.000491
-141205_at 462.4 P 0.003159
-141206_at 1301.9 P 0.000491
-141207_at 454.8 P 0.000944
-141208_at 438.6 P 0.000944
-141209_at 264.4 P 0.004591
-141210_at 65.6 A 0.150145
-141211_at 72.2 A 0.070073
-141212_at 1200 P 0.000491
-141213_at 13.7 A 0.635055
-141214_at 1944 P 0.000491
-141215_at 465.5 P 0.005504
-141216_at 538.9 P 0.002607
-141217_at 753.9 P 0.003159
-141218_at 2942.6 P 0.000491
-141219_at 283.9 P 0.010972
-!Sample_table_end
-
+^SAMPLE = Drosophila_T0-1
+!Sample_title = embryo at T0, biological rep1
+!Sample_supplementary_file = Drosophila_T0-1.CEL
+!Sample_source_name_ch1 = Drosophila embryos before nuclear cycle 9 (maternal transcripts)
+!Sample_organism_ch1 = Drosophila melanogaster
+!Sample_characteristics_ch1 = Genotype: yellow white and Oregon R parents
+!Sample_characteristics_ch1 = Age: embryos younger than nuclear cycle 9, i.e. before pole cells budding
+!Sample_treatment_protocol_ch1 = Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).
+!Sample_growth_protocol_ch1 = 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
+!Sample_label_ch1 = biotin
+!Sample_label_protocol_ch1 = Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
+!Sample_hyb_protocol = Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
+!Sample_scan_protocol = GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
+!Sample_description = Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
+!Sample_data_processing = The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
+!Sample_platform_id = GPL72
+#ID_REF =
+#VALUE = MAS5-calculated Signal intensity
+#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
+#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
+!Sample_table_begin
+ID_REF VALUE ABS_CALL DETECTION P-VALUE
+141200_at 36.6 A 0.818657
+141201_at 41.5 A 0.703191
+141202_at 607.3 P 0.000944
+141203_at 1509.1 P 0.000762
+141204_at 837.3 P 0.000613
+141205_at 363.2 P 0.003815
+141206_at 1193.6 P 0.000491
+141207_at 346.6 P 0.001165
+141208_at 257.8 P 0.006575
+141209_at 337.1 P 0.002607
+141210_at 48 A 0.150145
+141211_at 130.7 P 0.005504
+141212_at 1454.3 P 0.000491
+141213_at 21.2 A 0.635055
+142121_at 133.7 A 0.889551
+142122_at 275.3 A 0.611218
+142123_at 307.6 A 0.611218
+142124_at 132.6 A 0.437646
+142125_at 195.8 A 0.110449
+142126_at 174.1 A 0.681117
+142127_at 316.3 A 0.65838
+!Sample_table_end
+^SAMPLE = Drosophila_T0-2
+!Sample_title = embryo at T0, biological rep2
+!Sample_supplementary_file = Drosophila_T0-2.CEL
+!Sample_source_name_ch1 = Drosophila embryos before nuclear cycle 9 (maternal transcripts)
+!Sample_organism_ch1 = Drosophila melanogaster
+!Sample_characteristics_ch1 = Genotype: yellow white and Oregon R parents
+!Sample_characteristics_ch1 = Age: embryos younger than nuclear cycle 9, i.e. before pole cells budding
+!Sample_treatment_protocol_ch1 = Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).
+!Sample_growth_protocol_ch1 = 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
+!Sample_label_ch1 = biotin
+!Sample_label_protocol_ch1 = Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
+!Sample_hyb_protocol = Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
+!Sample_scan_protocol = GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
+!Sample_description = Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
+!Sample_data_processing = The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
+!Sample_platform_id = GPL72
+#ID_REF =
+#VALUE = MAS5-calculated Signal intensity
+#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
+#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
+!Sample_table_begin
+ID_REF VALUE ABS_CALL DETECTION P-VALUE
+141200_at 70.3 A 0.216313
+141201_at 38 A 0.635055
+141202_at 831.8 P 0.000613
+141203_at 2215.5 P 0.000944
+141204_at 965.6 P 0.000491
+141205_at 383.2 P 0.001432
+141206_at 1195 P 0.000491
+141207_at 413.7 P 0.000613
+141208_at 447.3 P 0.000762
+141209_at 294.4 P 0.004591
+141210_at 81.7 M 0.054711
+141211_at 84.9 P 0.005504
+141212_at 1456.4 P 0.000491
+141213_at 37 A 0.122747
+142121_at 133.7 A 0.889551
+142122_at 275.3 A 0.611218
+142123_at 307.6 A 0.611218
+142124_at 132.6 A 0.437646
+142125_at 195.8 A 0.110449
+142126_at 174.1 A 0.681117
+142127_at 316.3 A 0.65838
+!Sample_table_end
+^SAMPLE = Drosophila_T1-1
+!Sample_supplementary_file = Drosophila_T1-1.CEL
+!Sample_title = embryo at T1, biological rep1
+!Sample_source_name_ch1 = Drosophila embryos in slow phase of cellularisation
+!Sample_organism_ch1 = Drosophila melanogaster
+!Sample_characteristics_ch1 = Genotype: yellow white and Oregon R parents
+!Sample_characteristics_ch1 = Age: embryos in slow phase of cellularisation
+!Sample_treatment_protocol_ch1 = Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).
+!Sample_growth_protocol_ch1 = 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
+!Sample_label_ch1 = biotin
+!Sample_label_protocol_ch1 = Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
+!Sample_hyb_protocol = Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
+!Sample_scan_protocol = GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
+!Sample_description = Gene expression data from embryos in slow phase of cellularisation.
+!Sample_data_processing = The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
+!Sample_platform_id = GPL72
+#ID_REF =
+#VALUE = MAS5-calculated Signal intensity
+#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
+#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
+!Sample_table_begin
+ID_REF VALUE ABS_CALL DETECTION P-VALUE
+141200_at 20.8 A 0.801637
+141201_at 85.8 A 0.48748
+141202_at 704.8 P 0.000613
+141203_at 1036.6 P 0.000944
+141204_at 700.3 P 0.000491
+141205_at 462.4 P 0.003159
+141206_at 1301.9 P 0.000491
+141207_at 454.8 P 0.000944
+141208_at 438.6 P 0.000944
+141209_at 264.4 P 0.004591
+141210_at 65.6 A 0.150145
+141211_at 72.2 A 0.070073
+141212_at 1200 P 0.000491
+141213_at 13.7 A 0.635055
+142121_at 133.7 A 0.889551
+142122_at 275.3 A 0.611218
+142123_at 307.6 A 0.611218
+142124_at 132.6 A 0.437646
+142125_at 195.8 A 0.110449
+142126_at 174.1 A 0.681117
+142127_at 316.3 A 0.65838
+!Sample_table_end
+^SERIES = Dros_embryo_timecourse
+!Series_title = Expression data from early Drosophila embryo
+!Series_summary = Morphogenesis of epithelial tissues relies on the precise developmental control of cell polarity and architecture. In the early Drosophila embryo, the primary epithelium forms during cellularisation, following a tightly controlled genetic programme where specific sets of genes are up-regulated. Some of them, for instance, control membrane invagination between the nuclei anchored at the apical surface of the syncytium.
+!Series_summary = We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
+!Series_overall_design = Drosophila embryos were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of embryos at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected embryos according to morphological criteria at five time-points: before pole cell formation, i.e. before zygotic transcription (T0), during the slow phase (T1) and the fast phase (T2) of cellularisation and at the beginning (T3) and the end (T4) of gastrulation.
+!Series_type = time course
+!Series_contributor = Jane,Doe
+!Series_contributor = John,A,Smith
+!Series_contributor = Hans,van Elton
+!Series_contributor = John,Smithers Jr
+!Series_contributor = Jie,D,Chen
+!Series_sample_id = Drosophila_T0-1
+!Series_sample_id = Drosophila_T0-2
+!Series_sample_id = Drosophila_T1-1
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