rbbt-marq 1.0.0

data/install_scripts/GEO/series/GSE23.yaml

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+--- 
+:title: cdc15 block-release
+:description: |-
+  Yeast cells were blocked in telophase using a cdc15-2 temperature senstive mutant at restrictive temperature. The culture was then shifted to permissive temperature (25oC), and released into the cell cycle. Samples were then taken during the course of almost three full cell cycles.
+  This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97
+  Keywords: time-course
+:arrays: 
+  GSM1099: 
+    condition: cdc15 240 min
+  GSM896: 
+    condition: cdc15 030 min
+  GSM1056: 
+    condition: cdc15 160 min
+  GSM897: 
+    condition: cdc15 170 min
+  GSM1091: 
+    condition: cdc15 120 min
+  GSM1079: 
+    condition: cdc15 270 min
+  GSM898: 
+    condition: cdc15 150 min
+  GSM1092: 
+    condition: cdc15 140 min
+  GSM1036: 
+    condition: cdc15 090 min
+  GSM909: 
+    condition: cdc15 210 min
+  GSM1026: 
+    condition: cdc 15 010 min
+  GSM911: 
+    condition: cdc15 110 min
+  GSM900: 
+    condition: cdc15 130 min
+  GSM1072: 
+    condition: cdc15 250 min
+  GSM901: 
+    condition: cdc15 290 min
+  GSM1095: 
+    condition: cdc15 160 min
+  GSM1062: 
+    condition: cdc15 190 min
+  GSM1028: 
+    condition: cdc15 050 min
+  GSM1096: 
+    condition: cdc15 180 min
+  GSM1097: 
+    condition: cdc15 200 min
+  GSM1086: 
+    condition: cdc15 100 min
+  GSM1031: 
+    condition: cdc15 070 min
+  GSM1108: 
+    condition: cdc15 080 min
+  GSM1098: 
+    condition: cdc15 230 min
+  GSM1109: 
+    condition: cdc15 220 min
+:platform: GPL62

data/install_scripts/GEO/series/GSE2329.yaml

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+--- 
+:arrays: 
+  GSM43063: 
+    condition: ubp8 vs wt
+  GSM43052: 
+    condition: dot4 vs wt
+  GSM43064: 
+    condition: dot4ubp8 vs wt
+  GSM43053: 
+    condition: ubp8 vs wt
+  GSM43065: 
+    condition: dot4ubp8 vs wt
+  GSM43054: 
+    condition: dot4ubp8 vs wt
+  GSM43066: 
+    condition: dot4ubp8 vs wt
+  GSM43055: 
+    condition: dot4 vs wt
+  GSM43056: 
+    condition: ubp8 vs wt
+  GSM43057: 
+    condition: wt vs dot4ubp8 vs wt
+  GSM43058: 
+    condition: dot4 vs wt
+  GSM43059: 
+    condition: dot4 vs wt
+  GSM43060: 
+    condition: dot4 vs wt
+  GSM43049: 
+    condition: dot4 vs wt
+  GSM43061: 
+    condition: ubp8 vs wt
+  GSM43050: 
+    condition: ubp8 vs wt
+  GSM43062: 
+    condition: ubp8 vs wt
+  GSM43051: 
+    condition: dot4ubp8 vs wt
+:title: DOT4/dot4 null, UBP8/ubp8 null transcript arrays
+:description: |-
+  Comparison of DOT4/dot4 null cells, UBP8/ubp8 null cells, and DOT4UBP8/dot4ubp8 null cells in YEPD.
+  Keywords: other
+:platform: GPL1879

data/install_scripts/GEO/series/GSE2330.yaml

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+--- 
+:arrays: 
+  GSM43085: 
+    condition: wt vs wt dot4-1
+  GSM43074: 
+    condition: dot4-5 vs wt
+  GSM43086: 
+    condition: wt vs wt dot4-5
+  GSM43075: 
+    condition: dot4-5 vs wt
+  GSM43087: 
+    condition: wt vs wt dot4-5
+  GSM43076: 
+    condition: dot4-5 vs wt
+  GSM43088: 
+    condition: wt vs wt dot4-5
+  GSM43077: 
+    condition: dot4 vs wt Myc
+  GSM43089: 
+    condition: wt Myc-tagged vs wt dot4
+  GSM43078: 
+    condition: dot4 vs wt Myc
+  GSM43067: 
+    condition: dot4-1 vs wt
+  GSM43090: 
+    condition: wt Myc-tagged vs wt dot4
+  GSM43079: 
+    condition: dot4 vs wt Myc
+  GSM43068: 
+    condition: dot4-1 vs wt
+  GSM43091: 
+    condition: wt Myc-tagged vs wt dot4
+  GSM43080: 
+    condition: wt DOT4 vs wt DOT4-6Myc
+  GSM43069: 
+    condition: dot4-1 vs wt
+  GSM43092: 
+    condition: wt DOT4 Myc-tagged vs wt DOT4
+  GSM43081: 
+    condition: wt DOT4 vs wt DOT4-6Myc
+  GSM43093: 
+    condition: wt DOT4 Myc-tagged vs wt DOT4
+  GSM43082: 
+    condition: wt DOT4 vs wt DOT4-6Myc
+  GSM43094: 
+    condition: wt DOT4 Myc-tagged vs wt DOT4
+  GSM43083: 
+    condition: wt vs wt dot4-1
+  GSM43084: 
+    condition: wt vs wt dot4-1
+:title: DOT4/dot4-1 and DOT4/dot4-5 transcript arrays
+:description: |-
+  Comparison of DOT4-6Myc/dot4-1-6Myc cells, DOT4-6Myc/dot4-5-6Myc cells, DOT4-6Myc/dot4 null cells, DOT4-6Myc/DOT4 cells in YEPD
+  Keywords: other
+:platform: GPL1879

data/install_scripts/GEO/series/GSE2349.yaml

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+--- 
+:arrays: 
+  GSM43869: 
+    condition: H4 WT
+  GSM43897: 
+    condition: H4 K91A
+  GSM43865: 
+    condition: H4 K91A
+  GSM43866: 
+    condition: H4 K91A
+  GSM43867: 
+    condition: H4 WT
+  GSM43868: 
+    condition: H4 WT
+:title: Yeast Histone H4 K91A versus wild type
+:description: |-
+  Yeast strain containing either a histone H4 wild type or K91A allele was grown in YPD to mid-log phase and harvested.  Three replicates of each allele were performed
+  Keywords: repeat sample
+:platform: GPL90

data/install_scripts/GEO/series/GSE2412.yaml

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+--- 
+:arrays: 
+  GSM45510: 
+    condition: imazalil
+  GSM45499: 
+    condition: fenarimol
+  GSM45477: 
+    condition: cyprodinil
+  GSM45511: 
+    condition: fenbuconazole
+  GSM45500: 
+    condition: fenarimol
+  GSM45478: 
+    condition: cyprodinil
+  GSM45512: 
+    condition: fenbuconazole
+  GSM45513: 
+    condition: prochloraz
+  GSM45514: 
+    condition: imazalil
+  GSM45492: 
+    condition: dodemorph
+  GSM45515: 
+    condition: imazalil
+  GSM45493: 
+    condition: dodemorph
+  GSM45505: 
+    condition: prochloraz
+  GSM45494: 
+    condition: fenpropimorph
+  GSM45506: 
+    condition: triadimefon
+  GSM45495: 
+    condition: fenpropimorph
+  GSM45507: 
+    condition: triadimefon
+  GSM45496: 
+    condition: fenhexamid
+  GSM45508: 
+    condition: triadimefon
+  GSM45497: 
+    condition: fenhexamid
+  GSM45509: 
+    condition: imazalil
+  GSM45498: 
+    condition: fenhexamid
+:title: Agricultural sterol biosynthesis inhibitor fungicides
+:description: |-
+  agricultural sterol biosynthesis inhibitor fungicides
+  Keywords = agriculture
+  Keywords = ergosterol
+  Keywords = methionine
+  Keywords = fungicide
+  Keywords = Saccharomyces cerevisiae S288C
+  Keywords = biosynthesis
+  SUBMITTER_CITATION: Kagan IA, Michel A, Prause A, Scheffler BE, Pace P, Duke SO.  2005. Gene transcription profiles of Saccharomyces cerevisiae after treatment with plant protection fungicides that inhibit ergosterol biosynthesis. Pesticide Biochemistry and Physiology 82:133-153.
+  Keywords: other
+:platform: GPL1877

data/install_scripts/GEO/series/GSE2419.yaml

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+--- 
+:arrays: 
+  GSM45543: 
+    condition: 2h25umAFB
+  GSM45532: 
+    condition: 2h10umAFB
+  GSM45544: 
+    condition: 2h50umAFB
+  GSM45533: 
+    condition: 2h25umAFB
+  GSM45545: 
+    condition: 2h100umAFB
+  GSM45534: 
+    condition: 2h50umAFB
+  GSM45546: 
+    condition: 2h50umAFB
+  GSM45535: 
+    condition: 2h100umAFB
+  GSM45547: 
+    condition: 2h100umAFB
+  GSM45542: 
+    condition: 2h10umAFB
+:title: 2h dose response_AFB treatment
+:description: |-
+  RNA isolated from the 0, 10, 25, 50 and 100 micromolar AFB1 cultures at 120 min treatment was used for cDNA microarray experiments.  For each array hybridization experiment, RNAs from the treated sample and its corresponding time-matched control were co-hybridized to arrays and respectively quantified in different channels.  A dye swap strategy was used to eliminate the dye bias.
+  Keywords: dose response
+:platform: GPL1895

data/install_scripts/GEO/series/GSE2420.yaml

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+--- 
+:arrays: 
+  GSM45554: 
+    condition: 60min50umAFB
+  GSM45555: 
+    condition: 90min50umAFB
+  GSM45544: 
+    condition: 2h50umAFB
+  GSM45534: 
+    condition: 2h50umAFB
+  GSM45546: 
+    condition: 2h50umAFB
+  GSM45548: 
+    condition: 15min50umAFB
+  GSM45549: 
+    condition: 30min50umAFB
+  GSM45550: 
+    condition: 60min50umAFB
+  GSM45551: 
+    condition: 90min50umAFB
+  GSM45552: 
+    condition: 15min50umAFB
+  GSM45553: 
+    condition: 30min50umAFB
+:title: 50 uM AFB_time course
+:description: |-
+  RNA isolated from the cultures treated with 0 and 50 micromolar AFB1 at 15, 30, 60, 90, 120 min was used for microarray experiments. For each array hybridization experiment, RNAs from the treated sample and its corresponding time-matched control were co-hybridized to arrays and respectively quantified in different channels.  A dye swap strategy was used to eliminate the dye bias.
+  Keywords: time-course
+:platform: GPL1895

data/install_scripts/GEO/series/GSE2434.yaml

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+--- 
+:arrays: 
+  GSM42630: 
+    condition: wt2
+  GSM42631: 
+    condition: wt2
+  GSM42632: 
+    condition: wt2
+  GSM42621: 
+    condition: wt1
+  GSM42633: 
+    condition: hat1hat2
+  GSM42622: 
+    condition: wt1
+  GSM42634: 
+    condition: hat1hat2
+  GSM42623: 
+    condition: wt1
+  GSM42635: 
+    condition: hat1hat2
+  GSM42624: 
+    condition: hat1
+  GSM42625: 
+    condition: hat1
+  GSM42626: 
+    condition: hat1
+  GSM42627: 
+    condition: hat2
+  GSM42628: 
+    condition: hat2
+  GSM42629: 
+    condition: hat2
+:title: Hat mutants
+:description: |-
+  Transcriptomes from the hat1, hat2 and hat1 hat2 mutants in S288C yeast background.
+  Keywords: parallel sample
+:platform: GPL772

data/install_scripts/GEO/series/GSE2526.yaml

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+--- 
+:arrays: 
+  GSM48165: 
+    condition: highscan
+  GSM48166: 
+    condition: lowscan
+  GSM48167: 
+    condition: highscan
+  GSM48168: 
+    condition: lowscan
+  GSM48169: 
+    condition: highscan
+  GSM48170: 
+    condition: lowscan
+  GSM48171: 
+    condition: highscan
+  GSM48172: 
+    condition: lowscan
+:title: 30MPa, temp25,16h
+:description: "Series containes 4 independent experiments and high and low power scanns for each independent experiment.\n\
+  Genome-wide mRNA expression profiles of Saccharomyces cerevisiae growing under hydrostatic pressure were characterized.  We selected a hydrostatic pressure of 30 MPa at 25\xC2\xB0C because yeast cells were able to grow under these conditions, while cell size and complexity were increased after decompression.  Functional characterization of pressure-induced genes suggests that genes involved in protein metabolism and membrane metabolism were induced. The response to 30 MPa was significantly different from that observed under lethal conditions because protein degradation was not activated under 30 MPa pressure.  Strongly induced genes included those that contribute to membrane metabolism and which are also induced by detergents, oils, and membrane stabilizers.\n\
+  Keywords: repeat sample"
+:platform: GPL1951

data/install_scripts/GEO/series/GSE2579.yaml

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+--- 
+:arrays: 
+  GSM49659: 
+    condition: wt
+  GSM49660: 
+    condition: rrp6trf4
+  GSM49662: 
+    condition: wt
+  GSM49663: 
+    condition: wt
+  GSM49664: 
+    condition: rrp6
+  GSM49665: 
+    condition: rrp6
+:title: rrp6 delta and 	rrp6 delta, trf4 delta vs WT
+:description: "BMA64 rrp6 delta::HIS3 vs BMA64 WT (Mat a), grown at 30\xC2\xB0C to OD 0.6 in YPD.\n\
+  BMA64 rrp6 delta::URA3, trf4 delta::KAN vs BMA64 WT, grown at 30\xC2\xB0C to OD<0.6 in YPD.\n\
+  Keywords: other"
+:platform: GPL90

data/install_scripts/GEO/series/GSE2806.yaml

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+--- 
+:arrays: 
+  GSM60823: 
+    condition: wt
+  GSM60824: 
+    condition: acs2Ts1
+:title: Transcriptional profile of an acs2Ts1 mutant yeast
+:description: |-
+  Wild-type and the acs2Ts1 mutant yeasts were shifted from 25deg to 37deg. After 60 minutes, Yeasts were harvested and divided into 2 x 2 cell samples. Total RNAs were purified from 4 populations.
+  Keywords: WT vs mutant
+:platform: GPL2529

data/install_scripts/GEO/series/GSE2831.yaml

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+--- 
+:arrays: 
+  GSM61957: 
+    condition: rpb1-N488D
+  GSM61958: 
+    condition: rpb1-E1103G
+  GSM61960: 
+    condition: rpb1-E1230K
+  GSM61959: 
+    condition: rpb1-E1103G
+  GSM61961: 
+    condition: rpb1-E1230K
+  GSM61952: 
+    condition: rpb1-D261N
+  GSM61941: 
+    condition: RPB1
+  GSM61953: 
+    condition: rpb1-D261N
+  GSM61942: 
+    condition: RPB1
+  GSM61954: 
+    condition: rpb1-R320C
+  GSM61943: 
+    condition: rpb1-D260N
+  GSM61955: 
+    condition: rpb1-R320C
+  GSM61944: 
+    condition: rpb1-D260N
+  GSM61956: 
+    condition: rpb1-N488D
+:title: RPB1 mutants sensitive to 6-AU
+:description: |-
+  Gene expression profiling of RNA pol II mutants. In vivo effects of mutations in residues 260 (rudder), 261 (rudder), 320 (lid), 488 (close to catalytic center), 1230 (required for TFIIS stimulation) and 1103.
+  Keywords: Gene expression profiling of RNA pol II mutants
+:platform: GPL2547

data/install_scripts/GEO/series/GSE2832.yaml

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+--- 
+:arrays: 
+  GSM61948: 
+    condition: PoolA
+  GSM61950: 
+    condition: PoolB
+  GSM61949: 
+    condition: PoolA
+  GSM61951: 
+    condition: PoolAvsB
+  GSM61945: 
+    condition: PoolA
+:title: Improved statistical analysis of budding yeast TAG microarrays
+:description: |-
+  Yeast knockout collection TAG microarrays are an emergent platform for rapid, genome-wide functional characterization of yeast genes. We describe a method for analyzing two-color array data to efficiently represent differential knockout strain representation across two experimental conditions. Using a fully defined spike-in pool, we show that the sensitivity and specificity of this method exceed typical current approaches.
+  Keywords: Saccharomyces cerevisiae, yeast, self_vs_self, spike-in pools
+:platform: GPL1444