MARQ 0.0.1

data/install_scripts/GEO/series/GSE3815.yaml

@@ -0,0 +1,75 @@
+--- 
+:arrays: 
+  GSM87587: 
+    condition: RTG_10R40
+  GSM87576: 
+    condition: RTG_6R40
+  GSM87565: 
+    condition: RTG_3R0
+  GSM87554: 
+    condition: Sporulation_2h
+  GSM87577: 
+    condition: RTG_7R0
+  GSM87566: 
+    condition: RTG_3R20
+  GSM87555: 
+    condition: Sporulation_3h
+  GSM87578: 
+    condition: RTG_7R20
+  GSM87567: 
+    condition: RTG_3R40
+  GSM87556: 
+    condition: Sporulation_4h
+  GSM87579: 
+    condition: RTG_7R40
+  GSM87568: 
+    condition: RTG_4R0
+  GSM87557: 
+    condition: Sporulation_5h
+  GSM87580: 
+    condition: RTG_8R0
+  GSM87569: 
+    condition: RTG_4R20
+  GSM87558: 
+    condition: Sporulation_6h
+  GSM87581: 
+    condition: RTG_8R20
+  GSM87570: 
+    condition: RTG_4R40
+  GSM87559: 
+    condition: Sporulation_7h
+  GSM87582: 
+    condition: RTG_8R40
+  GSM87571: 
+    condition: RTG_5R0
+  GSM87560: 
+    condition: Sporulation_8h
+  GSM87583: 
+    condition: RTG_9R0
+  GSM87572: 
+    condition: RTG_5R20
+  GSM87561: 
+    condition: Sporulation_9h
+  GSM87584: 
+    condition: RTG_9R40
+  GSM87573: 
+    condition: RTG_5R40
+  GSM87562: 
+    condition: RTG_2R0
+  GSM87585: 
+    condition: RTG_10R0
+  GSM87574: 
+    condition: RTG_6R0
+  GSM87563: 
+    condition: RTG_2R20
+  GSM87586: 
+    condition: RTG_10R20
+  GSM87575: 
+    condition: RTG_6R20
+  GSM87564: 
+    condition: RTG_2R40
+:description: |-
+  We have used genome-wide expression profiling to investigate how budding yeast cells become committed to sporulation. Sporulating cells were transferred to growth medium at different stages of the process, and their transcription response was characterized. Most sporulation-induced genes were immediately down-regulated upon the transfer, even in committed cells that continued to sporulate. The metabolic-related transcription response of pre-committed cells or of mature spores transferred to growth medium was essentially the same as that of vegetative cells exposed to glucose. In contrast, committed cells elicited a unique, and dramatically different response. Our results suggest that cells ensure commitment to sporulation not by stabilizing the process, but by modulating their information processing in an active manner that may optimize sporulation in an environment-specific manner.
+  Keywords: Time course
+:platform: GPL3246
+:title: Sporulation_transfer_to_YPA1

data/install_scripts/GEO/series/GSE3817.yaml

@@ -0,0 +1,13 @@
+--- 
+:arrays: 
+  GSM87624: 
+    condition: spores
+  GSM87625: 
+    condition: sporesR15
+  GSM87626: 
+    condition: sporesR30
+:description: |-
+  We have used genome-wide expression profiling to investigate how budding yeast cells become committed to sporulation. Sporulating cells were transferred to growth medium at different stages of the process, and their transcription response was characterized. Most sporulation-induced genes were immediately down-regulated upon the transfer, even in committed cells that continued to sporulate. The metabolic-related transcription response of pre-committed cells or of mature spores transferred to growth medium was essentially the same as that of vegetative cells exposed to glucose. In contrast, committed cells elicited a unique, and dramatically different response. Our results suggest that cells ensure commitment to sporulation not by stabilizing the process, but by modulating their information processing in an active manner that may optimize sporulation in an environment-specific manner.
+  Keywords: Time course
+:platform: GPL3244
+:title: transfer_spores_to_YPD

data/install_scripts/GEO/series/GSE3818.yaml

@@ -0,0 +1,15 @@
+--- 
+:arrays: 
+  GSM87627: 
+    condition: Sporulation_5.5h
+  GSM87628: 
+    condition: RTG_5.5R0
+  GSM87629: 
+    condition: RTG_5.5R20
+  GSM87630: 
+    condition: RTG_5.5R40
+:description: |-
+  We have used genome-wide expression profiling to investigate how budding yeast cells become committed to sporulation. Sporulating cells were transferred to growth medium at different stages of the process, and their transcription response was characterized. Most sporulation-induced genes were immediately down-regulated upon the transfer, even in committed cells that continued to sporulate. The metabolic-related transcription response of pre-committed cells or of mature spores transferred to growth medium was essentially the same as that of vegetative cells exposed to glucose. In contrast, committed cells elicited a unique, and dramatically different response. Our results suggest that cells ensure commitment to sporulation not by stabilizing the process, but by modulating their information processing in an active manner that may optimize sporulation in an environment-specific manner.
+  Keywords: Time course
+:platform: GPL3245
+:title: Sporulation_SPS4_NDT80_transfer_to_YPD

data/install_scripts/GEO/series/GSE3819.yaml

@@ -0,0 +1,13 @@
+--- 
+:arrays: 
+  GSM87631: 
+    condition: Sporulation_6h_2
+  GSM87632: 
+    condition: RTG_6R20_2
+  GSM87633: 
+    condition: RTG_6R40_2
+:description: |-
+  We have used genome-wide expression profiling to investigate how budding yeast cells become committed to sporulation. Sporulating cells were transferred to growth medium at different stages of the process, and their transcription response was characterized. Most sporulation-induced genes were immediately down-regulated upon the transfer, even in committed cells that continued to sporulate. The metabolic-related transcription response of pre-committed cells or of mature spores transferred to growth medium was essentially the same as that of vegetative cells exposed to glucose. In contrast, committed cells elicited a unique, and dramatically different response. Our results suggest that cells ensure commitment to sporulation not by stabilizing the process, but by modulating their information processing in an active manner that may optimize sporulation in an environment-specific manner.
+  Keywords: Time course
+:platform: GPL3245
+:title: Sporulation_sum1_del_transfer_to_YPD

data/install_scripts/GEO/series/GSE3820.yaml

@@ -0,0 +1,61 @@
+--- 
+:arrays: 
+  GSM87653: 
+    condition: 6r20
+  GSM87642: 
+    condition: 2r20
+  GSM87654: 
+    condition: 6r2h20
+  GSM87643: 
+    condition: 2r1h20
+  GSM87655: 
+    condition: 7r20
+  GSM87644: 
+    condition: 2r2h20
+  GSM87656: 
+    condition: 7r2h20
+  GSM87645: 
+    condition: 3r20
+  GSM87634: 
+    condition: 2s
+  GSM87657: 
+    condition: 8r20
+  GSM87646: 
+    condition: 3r2h20
+  GSM87635: 
+    condition: 3s
+  GSM87658: 
+    condition: 8r1h20
+  GSM87647: 
+    condition: 4r20
+  GSM87636: 
+    condition: 4s
+  GSM87659: 
+    condition: 9r20
+  GSM87648: 
+    condition: 4r1h20
+  GSM87637: 
+    condition: 5s
+  GSM87660: 
+    condition: 9r1h20
+  GSM87649: 
+    condition: 4r2h20
+  GSM87638: 
+    condition: 6s
+  GSM87650: 
+    condition: 5r20
+  GSM87639: 
+    condition: 7s
+  GSM87651: 
+    condition: 5r1h20
+  GSM87640: 
+    condition: 8s
+  GSM87652: 
+    condition: 5r2h20
+  GSM87641: 
+    condition: 9s
+:description: |-
+  We have used genome-wide expression profiling to investigate how budding yeast cells become committed to sporulation. Sporulating cells were transferred to growth medium at different stages of the process, and their transcription response was characterized. Most sporulation-induced genes were immediately down-regulated upon the transfer, even in committed cells that continued to sporulate. The metabolic-related transcription response of pre-committed cells or of mature spores transferred to growth medium was essentially the same as that of vegetative cells exposed to glucose. In contrast, committed cells elicited a unique, and dramatically different response. Our results suggest that cells ensure commitment to sporulation not by stabilizing the process, but by modulating their information processing in an active manner that may optimize sporulation in an environment-specific manner.
+  Keywords: Time course
+:platform: GPL3245
+:title: Sporulation_transfer_to_YPA2

data/install_scripts/GEO/series/GSE3821.yaml

@@ -0,0 +1,55 @@
+--- 
+:arrays: 
+  GSM87675: 
+    time: "120"
+    treatment: glu3
+  GSM87664: 
+    time: "300"
+    treatment: glu1
+  GSM87676: 
+    time: "300"
+    treatment: glu3
+  GSM87665: 
+    time: "330"
+    treatment: glu1
+  GSM87666: 
+    time: "0"
+    treatment: glu2
+  GSM87667: 
+    time: "30"
+    treatment: glu2
+  GSM87668: 
+    time: "60"
+    treatment: glu2
+  GSM87669: 
+    time: "120"
+    treatment: glu2
+  GSM87670: 
+    time: "300"
+    treatment: glu2
+  GSM87671: 
+    time: "330"
+    treatment: glu2
+  GSM87672: 
+    time: "0"
+    treatment: glu3
+  GSM87661: 
+    time: "0"
+    treatment: glu1
+  GSM87673: 
+    time: "30"
+    treatment: glu3
+  GSM87662: 
+    time: "120"
+    treatment: glu1
+  GSM87674: 
+    time: "60"
+    treatment: glu3
+  GSM87663: 
+    time: "210"
+    treatment: glu1
+:description: |-
+  Study of the short term (within the first 330 seconds)  transcriptional response of S.cerevisiae  upon a sudden addition of glucose.
+  Keywords: glucose pulse, chemostat culture, glucose catabolite repression
+:platform: GPL90
+:title: Short term perturbation

data/install_scripts/GEO/series/GSE3844.yaml

@@ -0,0 +1,11 @@
+--- 
+:arrays: 
+  GSM88058: 
+    condition: yeast_nutrient variation
+  GSM88059: 
+    condition: yeast_nutrient variation
+:description: |-
+  This experiment compares the transcriptional profiles of a WT yeast strain grown in either 2% glucose or 3% pyruvate.  The goal was to identify genes whose expression is either induced or repressed by glucose (catabolite repression).
+  Keywords: nutrient response
+:platform: GPL884
+:title: Yeast carbon source comparison

data/install_scripts/GEO/series/GSE3853.yaml

@@ -0,0 +1,31 @@
+--- 
+:arrays: 
+  GSM88170: 
+    condition: nup84-gcr1 vs wt
+  GSM88172: 
+    condition: nup84-gcr1 vs wt
+  GSM88162: 
+    condition: gcr1 vs wt
+  GSM88163: 
+    condition: gcr1 vs wt
+  GSM88164: 
+    condition: gcr1 vs wt
+  GSM88165: 
+    condition: nup84 vs wt
+  GSM88166: 
+    condition: nup84 vs wt
+  GSM88155: 
+    condition: gcr1 vs wt
+  GSM88189: 
+    condition: nup84-gcr1 vs wt
+  GSM88167: 
+    condition: nup84 vs wt
+  GSM88168: 
+    condition: nup84 vs wt
+  GSM88169: 
+    condition: nup84-gcr1 vs wt
+:description: |-
+  This experiment compares the transcriptional response of yeast cells to the deletion of Gcr1, Nup84, or both, to isogenic wild type strains grown in YPD at 23C.  The goal was to identify misregulated target genes and analyze the functional classifications of those targets.
+  Keywords: cell type comparison (knock-outs)
+:platform: GPL2883
+:title: Transcriptome response to the deletion of Gcr1, Nup84 or Nup84 & Gcr1 (double deletion)

data/install_scripts/GEO/series/GSE3935.yaml

@@ -0,0 +1,12 @@
+--- 
+:arrays: 
+  GSM90166: 
+    condition: Hydrostatic pressure
+  GSM90167: 
+    condition: Hydrostatic pressure
+:description: |-
+  S. cerevisiae Y440 Mat a leu2 was grown in YEPD at 28 degrees C with aeration to exponential growth phase and was subjected to a hydrostatic pressure of 50 and 200 MPa for 30 minutes at room temperature. Total RNA was extracted using phenol/chloroform and further precipitated with 3 M sodium acetate / absolute ethanol. Extracted RNA samples were treated for 10 min with 0.5 U of RNAse-free DNAse I / ]g RNA at 37 oC to remove any residual genomic DNA. RNA pellets were washed in 70 % ethanol and resuspended in DEPC treated water. Purified mRNA from pressurized and unpressurized cells was reversed-transcribed, labeled with fluorescent-tagged nucleotides, and hybridized against a common refernce pool of mRNA for 18 h at 65 0C on cDNA microarray. After several washes, arrays were scanned using a commercially available scanning laser microscope (GenePix 4000) from Axon Instruments (Foster City, CA), the data obtained was normalized (mean value) applying a linear regression method.
+  An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract
+  Keywords: Computed
+:platform: GPL2658
+:title: Response to high hydrostatic pressure

data/install_scripts/GEO/series/GSE3969.yaml

@@ -0,0 +1,14 @@
+--- 
+:arrays: 
+  GSM90540: 
+    condition: puf3 vs wt
+  GSM90541: 
+    condition: puf3 vs wt
+  GSM90542: 
+    condition: puf3 vs wt
+:description: |-
+  Three independent experiments: S. cervisiae wild-type (BY4741) and Puf3 mutant cells were grown in minimal medium supplemented with 3% glycerol. Cells were harvested in mid-log phase by centrifugation and total RNA was prepared by hot-phenol extraction. cDNA was prepared with oligo-dT and using a mixture of amino-allyl dUTP and dNTPs, fluorescently labeled (Cy3= wild-type, Cy5 = mutant) and hybridize on S. cerevisiae DNA microarray.
+  Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
+  Keywords: Logical Set
+:platform: GPL3300
+:title: Puf3delta vs. wild type comparison

data/install_scripts/GEO/series/GSE4049.yaml

@@ -0,0 +1,80 @@
+--- 
+:arrays: 
+  GSM91888: 
+    condition: 90caf2
+  GSM91877: 
+    condition: cfw15_2
+  GSM91437: 
+    condition: 90caf2
+  GSM91426: 
+    condition: cfw90_1
+  GSM91890: 
+    condition: 15caf1
+  GSM91889: 
+    condition: 90caf1
+  GSM91878: 
+    condition: cfw15_1
+  GSM91438: 
+    condition: 90caf1
+  GSM91427: 
+    condition: cfw5_2
+  GSM91891: 
+    condition: 15caf2
+  GSM91880: 
+    condition: cfw5_2
+  GSM91440: 
+    condition: 5caf1
+  GSM91439: 
+    condition: 5caf2
+  GSM91428: 
+    condition: cfw5_1
+  GSM91892: 
+    condition: 5caf2
+  GSM91881: 
+    condition: cfw5_1
+  GSM91430: 
+    condition: cfw15_1
+  GSM91429: 
+    condition: cfw15_2
+  GSM91893: 
+    condition: 5caf1
+  GSM91882: 
+    condition: cr15_2
+  GSM91442: 
+    condition: 15caf2
+  GSM91431: 
+    condition: cr90_2
+  GSM91894: 
+    condition: cfw90_2
+  GSM91883: 
+    condition: cr15_1
+  GSM91443: 
+    condition: 15caf1
+  GSM91432: 
+    condition: cr90_1
+  GSM91884: 
+    condition: cr90_1
+  GSM91444: 
+    condition: cfw90_2
+  GSM91433: 
+    condition: cr5_2
+  GSM91885: 
+    condition: cr90_2
+  GSM91434: 
+    condition: cr5_1
+  GSM91886: 
+    condition: cr5_2
+  GSM91435: 
+    condition: cr15_2
+  GSM91887: 
+    condition: cr5_1
+  GSM91876: 
+    condition: cfw90_1
+  GSM91436: 
+    condition: cr15_1
+:description: |-
+  Caffeine is a natural purine analog that elicits pleiotropic effects, which ultimately lead to cell death by a mechanism that is still largely uncharacterized. This drug can activate the PKC1-MAPK cell integrity pathway, as shown by phosphorylation of Mpk1 kinase. However, and contrary to expectation, the caffeine-induced hyperphosphorylation of Mpk1 was accompanied by a negligible activation of its downstream targets Rlm1 and SBF transcription factors, which suggested that the fortification of the cell wall induced by caffeine was independent on the MAP kinase activation. This result was consistent with the finding that the loss of RLM1 had no consequence on the increased resistance of caffeine-treated cells to zymolyase, and was further consolidated by a genome-wide microarray analysis showing that, contrary to the cell wall drugs Congo Red and Calcofluor white, caffeine did not cause upregulation of Rlm1-dependent genes encoding cell wall remodeling enzymes. Interestingly, this global expression analysis revealed a striking resemblance of the transcriptomic responses to caffeine with those of rapamycin, a potent inhibitor of the TOR1 and TOR2 kinases. Consistent with this analysis, we found that the caffeine-induced phosphorylation of Mpk1 was lost in a tor1(delta) mutant but it was conserved in a TOR1-1 strain bearing a rapamycin-insensitive Tor1 kinase. Also, and contrary to the mechanism by which rapamycin led to activation of the PKC pathway, the caffeine-dependent process did not necessitate cell wall sensors and was completely abolished upon deletion of ROM2 encoding a GDP/GTP exchange factor of the Rho1-PKC pathway. Moreover, addition of caffeine to yeast cells resulted in a transient drop in intracellular cAMP, and this effect was not observed in a rom2(delta) mutant. In summary, our results revealed that Tor1 is a potential direct target of caffeine in yeast, whose inhibition leads to activation of the Pkc1-Mpk1 kinase cascade and inhibition of the Ras/cAMP pathway, and that for this specific case, the cross-talk between these signaling pathways is mediated by Rom2. These results may have broad implication for our understanding of caffeine effects in analogous regulatory networks in mammalian cells.
+  Key words: caffeine, antifungal drugs, cell wall, transcript profiling, TOR, PKC1, RAS/cAMP.
+  Keywords: time course, dose response
+:platform: GPL3250
+:title: Time-course studies of three cell wall interfering drugs on gene expression in yeast

data/install_scripts/GEO/series/GSE4144.yaml

@@ -0,0 +1,9 @@
+--- 
+:arrays: 
+  GSM94607: 
+    condition: acs2-Ts8
+:description: |-
+  Obtain synthetic lethality/slow growth gene interactors of acs2-Ts8
+  Keywords: gene mutation
+:platform: GPL1444
+:title: Synthetic lethality/slow growth with acs2-Ts8

data/install_scripts/GEO/series/GSE4261.yaml

@@ -0,0 +1,59 @@
+--- 
+:arrays: 
+  GSM97179: 
+    condition: Sce27
+  GSM97168: 
+    condition: Sce26
+  GSM97157: 
+    condition: Sce1113
+  GSM97180: 
+    condition: Sce28
+  GSM97158: 
+    condition: Sce17
+  GSM97181: 
+    condition: Sce28
+  GSM97159: 
+    condition: Sce17
+  GSM97182: 
+    condition: Sce509
+  GSM97160: 
+    condition: Sce17
+  GSM97183: 
+    condition: Sce509
+  GSM97161: 
+    condition: Sce17
+  GSM97162: 
+    condition: Sce18
+  GSM97163: 
+    condition: Sce18
+  GSM97152: 
+    condition: Sce1060
+  GSM97175: 
+    condition: Sce26
+  GSM97164: 
+    condition: Sce19
+  GSM97153: 
+    condition: Sce1060
+  GSM97176: 
+    condition: Sce27
+  GSM97165: 
+    condition: Sce19
+  GSM97154: 
+    condition: Sce1089
+  GSM97177: 
+    condition: Sce27
+  GSM97166: 
+    condition: Sce26
+  GSM97155: 
+    condition: Sce1089
+  GSM97178: 
+    condition: Sce27
+  GSM97167: 
+    condition: Sce26
+  GSM97156: 
+    condition: Sce1113
+:description: |-
+  Genome-wide assays to test the interaction between two independently evolved mechanisms of fluconazole resistance
+  Keywords: Comparative genomic hybridization
+:platform: GPL3458
+:title: Antagonism between two mechanisms of antifungal drug resistance