rbbt-marq 1.0.0

data/install_scripts/GEO/series/GSE5290.yaml

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+--- 
+:description: |-
+  The highly conserved protein eIF5A found in archaea and all eucaryotes uniquely contains the posttranslationally formed amino acid hypusine. Despite being essential the functions of this protein and its modification remain unclear. To gain more insight into these functions temperature sensitive mutants of the human EIF5A1 were characterized in the yeast Saccharomyces cerevisiae.
+  EIF5A is proposed to be an RNA binding protein. Thus, we used microarrays to identify special RNA subsets of up- and downregulation that are influenced by a limited eIF5A function in strains expressing a point mutated form of eIF5A.
+  Keywords: two sets of four biological replicates of wild-type and mutant strains
+:title: Temperature sensitive eIF5A mutant shows accumulation of transcripts targeted to the Nonsense Mediated Decay pathway
+:arrays: 
+  GSM119755: 
+    condition: wt
+  GSM119756: 
+    condition: wt
+  GSM119757: 
+    condition: wt
+  GSM119758: 
+    condition: wt
+  GSM119751: 
+    condition: V81G
+  GSM119752: 
+    condition: V81G
+  GSM119753: 
+    condition: V81G
+  GSM119754: 
+    condition: V81G
+:platform: GPL90

data/install_scripts/GEO/series/GSE5376.yaml

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+--- 
+:description: |-
+  Transcription profiles across the cell cycle of yox1 deleted yeast cells. BY2399 cells (yox1 delete cells isogenic with W303a) were arrested with alpha factor in YEPD media. After release from arrest cells were sampled every 5 min for 2 hr.
+  Keywords: cell cycle time course
+:title: Cell cycle of yeast deleted for yox1
+:arrays: 
+  GSM120185: 
+    time: yox1 90
+  GSM120174: 
+    time: yox1 35
+  GSM120053: 
+    time: yox1 85
+  GSM120042: 
+    time: yox1 30
+  GSM120186: 
+    time: yox1 95
+  GSM120175: 
+    time: yox1 40
+  GSM120054: 
+    time: yox1 90
+  GSM120043: 
+    time: yox1 35
+  GSM120187: 
+    time: yox1 100
+  GSM120176: 
+    time: yox1 45
+  GSM120055: 
+    time: yox1 95
+  GSM120044: 
+    time: yox1 40
+  GSM120188: 
+    time: yox1 105
+  GSM120177: 
+    time: yox1 50
+  GSM120056: 
+    time: yox1 100
+  GSM120045: 
+    time: yox1 45
+  GSM120190: 
+    time: yox1 115
+  GSM120189: 
+    time: yox1 110
+  GSM120178: 
+    time: yox1 55
+  GSM120167: 
+    time: yox1 0
+  GSM120057: 
+    time: yox1 105
+  GSM120046: 
+    time: yox1 50
+  GSM120191: 
+    time: yox1 120
+  GSM120180: 
+    time: yox1 65
+  GSM120179: 
+    time: yox1 60
+  GSM120168: 
+    time: yox1 5
+  GSM120058: 
+    time: yox1 110
+  GSM120047: 
+    time: yox1 55
+  GSM120036: 
+    time: yox1 0
+  GSM120181: 
+    time: yox1 70
+  GSM120170: 
+    time: yox1 15
+  GSM120169: 
+    time: yox1 10
+  GSM120060: 
+    time: yox1 120
+  GSM120059: 
+    time: yox1 115
+  GSM120048: 
+    time: yox1 60
+  GSM120037: 
+    time: yox1 5
+  GSM120182: 
+    time: yox1 75
+  GSM120171: 
+    time: yox1 20
+  GSM120050: 
+    time: yox1 70
+  GSM120049: 
+    time: yox1 65
+  GSM120038: 
+    time: yox1 10
+  GSM120183: 
+    time: yox1 80
+  GSM120172: 
+    time: yox1 25
+  GSM120051: 
+    time: yox1 75
+  GSM120040: 
+    time: yox1 20
+  GSM120039: 
+    time: yox1 15
+  GSM120184: 
+    time: yox1 85
+  GSM120173: 
+    time: yox1 30
+  GSM120052: 
+    time: yox1 80
+  GSM120041: 
+    time: yox1 25
+:platform: GPL1914

data/install_scripts/GEO/series/GSE5575.yaml

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+--- 
+:description: |-
+  This experiment was done to detect the transcriptomic defects in the gcr1 null mutant, relative to an isogenic wild type, in the immediate response to glucose.
+  Keywords: time course
+:title: Response of gcr1 null mutant to glucose
+:arrays: 
+  GSM129828: 
+    condition: Yeast_null mutant 60min
+  GSM129826: 
+    condition: Yeast_null mutant 0min
+  GSM129827: 
+    condition: Yeast_null mutant 20min
+:platform: GPL884

data/install_scripts/GEO/series/GSE5835.yaml

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+--- 
+:description: |-
+  Gene expression analysis of a time course experiment of a synthetic must (nitrogen-rich) fermentation by a natural wine yeast.
+  Keywords: Time course
+:title: Normal Fermentation
+:arrays: 
+  GSM113332: 
+    condition: NF t2
+  GSM113333: 
+    condition: NF t2
+  GSM113334: 
+    condition: NF t3
+  GSM113335: 
+    condition: NF t3
+  GSM113336: 
+    condition: NF t3
+  GSM113325: 
+    condition: NF t1
+  GSM113326: 
+    condition: NF t1
+  GSM113327: 
+    condition: NF t1
+  GSM113329: 
+    condition: NF t2
+:platform: GPL3763

data/install_scripts/GEO/series/GSE5836.yaml

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+--- 
+:description: |-
+  Gene expression analysis of a time course experiment of a synthetic must (nitrogen-poor) fermentation by a natural wine yeast.
+  Keywords: Time course
+:title: Sluggish Fermentation
+:arrays: 
+  GSM113397: 
+    condition: SFt8
+  GSM113386: 
+    condition: SFt4
+  GSM113398: 
+    condition: SFt8
+  GSM113387: 
+    condition: SFt5
+  GSM113388: 
+    condition: SFt5
+  GSM113390: 
+    condition: SFt6
+  GSM113389: 
+    condition: SFt5
+  GSM113391: 
+    condition: SFt6
+  GSM113392: 
+    condition: SFt6
+  GSM113393: 
+    condition: SFt7
+  GSM113394: 
+    condition: SFt7
+  GSM113383: 
+    condition: SFt4
+  GSM113395: 
+    condition: SFt7
+  GSM113384: 
+    condition: SFt4
+  GSM113396: 
+    condition: SFt8
+:platform: GPL3763

data/install_scripts/GEO/series/GSE5837.yaml

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+--- 
+:description: |-
+  Gene expression analysis of a time course experiment of a synthetic must (nitrogen-poor) fermentation by a natural wine yeast, supplemented at 72 hours with 200 mg/l of nitrogen
+  Keywords: Time course
+:title: Recovered Fermentation
+:arrays: 
+  GSM113407: 
+    condition: SF t11
+  GSM113386: 
+    condition: SF t4
+  GSM113387: 
+    condition: SF t5
+  GSM113399: 
+    condition: SF t9
+  GSM113388: 
+    condition: SF t5
+  GSM113400: 
+    condition: SF t9
+  GSM113389: 
+    condition: SF t5
+  GSM113401: 
+    condition: SF t9
+  GSM113402: 
+    condition: SF t10
+  GSM113403: 
+    condition: SF t10
+  GSM113404: 
+    condition: SF t10
+  GSM113383: 
+    condition: SF t4
+  GSM113405: 
+    condition: SF t11
+  GSM113384: 
+    condition: SF t4
+  GSM113406: 
+    condition: SF t11
+:platform: GPL3763

data/install_scripts/GEO/series/GSE5938.yaml

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+--- 
+:arrays: 
+  GSM137882: 
+    treatment: yap6
+  GSM137859: 
+    treatment: tec1-sok2
+  GSM63865: 
+    treatment: wt
+  GSM137838: 
+    treatment: cup9
+  GSM137861: 
+    treatment: tec1-skn7
+  GSM137883: 
+    treatment: yap6
+  GSM63866: 
+    treatment: 0mM cAMP
+  GSM137840: 
+    treatment: cup9
+  GSM137839: 
+    treatment: cup9
+  GSM63867: 
+    treatment: 0mM cAMP
+  GSM137841: 
+    treatment: cup9
+  GSM137862: 
+    treatment: tec1-skn7
+  GSM137884: 
+    treatment: cup9-yap6
+  GSM63868: 
+    treatment: 0.5mM cAMP
+  GSM137842: 
+    treatment: sfl1
+  GSM137863: 
+    treatment: cup9-sfl1
+  GSM137885: 
+    treatment: cup9-yap6
+  GSM63870: 
+    treatment: 1mM cAMP
+  GSM137843: 
+    treatment: sfl1
+  GSM137864: 
+    treatment: cup9-sfl1
+  GSM137886: 
+    treatment: cup9-yap6
+  GSM63871: 
+    treatment: 2mM cAMP
+  GSM137823: 
+    treatment: Wild-type yeast form
+  GSM137844: 
+    treatment: sfl1
+  GSM137865: 
+    treatment: cup9-sfl1
+  GSM137887: 
+    treatment: sfl1-yap6
+  GSM63872: 
+    treatment: mM cAMP
+  GSM137824: 
+    treatment: Wild-type yeast form
+  GSM137845: 
+    treatment: sok2
+  GSM137866: 
+    treatment: cup9-sok2
+  GSM137890: 
+    treatment: sok2-yap6
+  GSM137888: 
+    treatment: sfl1-yap6
+  GSM137825: 
+    treatment: Wild-type yeast form
+  GSM137846: 
+    treatment: sok2
+  GSM137867: 
+    treatment: cup9-sok2
+  GSM63873: 
+    treatment: ira1
+  GSM137891: 
+    treatment: sok2-yap6
+  GSM137889: 
+    treatment: sfl1-yap6
+  GSM137870: 
+    treatment: cup9-skn7
+  GSM137826: 
+    treatment: Wild-type yeast form
+  GSM137847: 
+    treatment: sok2
+  GSM137868: 
+    treatment: cup9-sok2
+  GSM63874: 
+    treatment: ira1
+  GSM137892: 
+    treatment: sok2-yap6
+  GSM137871: 
+    treatment: cup9-skn7
+  GSM137869: 
+    treatment: cup9-skn7
+  GSM137848: 
+    treatment: skn7
+  GSM63875: 
+    treatment: ira1RA
+  GSM137827: 
+    treatment: Wild-type yeast form
+  GSM137850: 
+    treatment: skn7
+  GSM137872: 
+    treatment: sfl1-sok2
+  GSM63876: 
+    treatment: ira1RA
+  GSM137828: 
+    treatment: Wild-type yeast form
+  GSM137849: 
+    treatment: skn7
+  GSM63877: 
+    treatment: ira2
+  GSM137830: 
+    treatment: Wild-type filamentous form
+  GSM137829: 
+    treatment: Wild-type filamentous form
+  GSM137851: 
+    treatment: tec1-cup9
+  GSM137873: 
+    treatment: sfl1-sok2
+  GSM63878: 
+    treatment: ira2
+  GSM137831: 
+    treatment: Wild-type filamentous form
+  GSM137852: 
+    treatment: tec1-cup9
+  GSM137874: 
+    treatment: sfl1-sok2
+  GSM63880: 
+    treatment: ras2v19
+  GSM63879: 
+    treatment: ras2v19
+  GSM137832: 
+    treatment: tec1
+  GSM137853: 
+    treatment: tec1-cup9
+  GSM137875: 
+    treatment: sfl1-skn7
+  GSM63881: 
+    treatment: ras2a22
+  GSM137833: 
+    treatment: tec1
+  GSM137854: 
+    treatment: tec1-sfl1
+  GSM137876: 
+    treatment: sfl1-skn7
+  GSM63861: 
+    treatment: wt
+  GSM63882: 
+    treatment: ras2a22
+  GSM137834: 
+    treatment: tec1
+  GSM137855: 
+    treatment: tec1-sfl1
+  GSM137877: 
+    treatment: sfl1-skn7
+  GSM137835: 
+    treatment: tec1
+  GSM137856: 
+    treatment: tec1-sfl1
+  GSM63862: 
+    treatment: wt
+  GSM137880: 
+    treatment: sok2-skn7
+  GSM137878: 
+    treatment: sok2-skn7
+  GSM137836: 
+    treatment: tec1
+  GSM137857: 
+    treatment: tec1-sok2
+  GSM137881: 
+    treatment: yap6
+  GSM137879: 
+    treatment: sok2-skn7
+  GSM137837: 
+    treatment: cup9
+  GSM137860: 
+    treatment: tec1-skn7
+  GSM137858: 
+    treatment: tec1-sok2
+  GSM63864: 
+    treatment: wt
+:description: |-
+  We construced combinations of genetic deletions to infer genetic interactions in genomic expression data.
+  Keywords: combinatorial genetic perturbations
+:title: Expression data for filamentous-form yeast with genetic perturbations
+:platform: GPL90

data/install_scripts/GEO/series/GSE600.yaml

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+--- 
+:title: S. cerevisiae mutant with a constitutively activated Ras/cAMP pathway
+:description: |-
+  Comparison of the transcriptomes of Saccharomyces cerevisiae wild type FY23 and a PDE2 deletion mutant DJ28.
+  Keywords = PDE2
+  Keywords = Ras/cAMP pathway
+  Keywords: other
+:arrays: 
+  GSM9174: 
+    condition: DLJ
+  GSM9175: 
+    condition: DLJ
+  GSM9142: 
+    condition: DLJ
+  GSM9176: 
+    condition: DLJ
+  GSM9177: 
+    condition: DLJ
+  GSM9178: 
+    condition: DLJ
+  GSM9179: 
+    condition: DLJ
+  GSM9180: 
+    condition: DLJ
+  GSM9181: 
+    condition: DLJ
+  GSM9182: 
+    condition: DLJ
+:platform: GPL422