MARQ 0.0.1

data/install_scripts/GEO/series/GSE3503.yaml

@@ -0,0 +1,19 @@
+--- 
+:title: Rapid tRNA decay can result from lack of non-essential modifications
+:description: |-
+  A microarray tiling approach was utilized to assay tRNA modifications by comparing hybridization affinity of tRNA-modification mutants to wild-type across all annotated yeast tRNAs.
+  Keywords: Assaying noncoding RNA modifications
+:arrays: 
+  GSM80015: 
+    mutant: pus7
+  GSM80016: 
+    mutant: trm8
+  GSM80017: 
+    mutant: dus3
+  GSM80018: 
+    mutant: trm8-pus7
+  GSM80019: 
+    mutant: trm8-dus3
+  GSM80020: 
+    mutant: trm8-trm4
+:platform: GPL3013

data/install_scripts/GEO/series/GSE3683.yaml

@@ -0,0 +1,83 @@
+--- 
+:title: Oxidative Stress 30-min interval
+:description: |-
+  Determine if yeast cell in stationary-phase cultures respond to oxidative stress
+  Keywords: time-course
+:arrays: 
+  GSM84452: 
+    time: YS8
+  GSM84441: 
+    time: YS2.5
+  GSM84430: 
+    time: YS5
+  GSM84419: 
+    time: YS0
+  GSM84442: 
+    time: YS3
+  GSM84431: 
+    time: YS5.5
+  GSM84420: 
+    time: YS0
+  GSM84443: 
+    time: YS3.5
+  GSM84432: 
+    time: YS6
+  GSM84421: 
+    time: YS0.5
+  GSM84444: 
+    time: YS4
+  GSM84433: 
+    time: YS6.5
+  GSM84422: 
+    time: YS1
+  GSM84445: 
+    time: YS4.5
+  GSM84434: 
+    time: YS7
+  GSM84423: 
+    time: YS1.5
+  GSM84446: 
+    time: YS5
+  GSM84435: 
+    time: YS7.5
+  GSM84424: 
+    time: YS2
+  GSM84447: 
+    time: YS5.5
+  GSM84436: 
+    time: YS8
+  GSM84425: 
+    time: YS2.5
+  GSM84448: 
+    time: YS6
+  GSM84437: 
+    time: YS0.5
+  GSM84426: 
+    time: YS3
+  GSM84415: 
+    time: YS0
+  GSM84449: 
+    time: YS6.5
+  GSM84438: 
+    time: YS1
+  GSM84427: 
+    time: YS3.5
+  GSM84416: 
+    time: YS0
+  GSM84450: 
+    time: YS7
+  GSM84439: 
+    time: YS1.5
+  GSM84428: 
+    time: YS4
+  GSM84417: 
+    time: YS0
+  GSM84451: 
+    time: YS7.5
+  GSM84440: 
+    time: YS2
+  GSM84429: 
+    time: YS4.5
+  GSM84418: 
+    time: YS0
+:platform: GPL3153

data/install_scripts/GEO/series/GSE3684.yaml

@@ -0,0 +1,19 @@
+--- 
+:title: Hot phenol
+:description: |-
+  Determine differences between RNA isolation methods.
+  Keywords: Comparison of RNA isolation techniques
+:arrays: 
+  GSM84507: 
+    condition: YSProtKRNAIso0min
+  GSM84508: 
+    condition: YSProtKRNAIso0min
+  GSM84503: 
+    condition: YSOusRNAIso0min
+  GSM84504: 
+    condition: YSOusRNAIso0min
+  GSM84505: 
+    condition: YSHotPhenolRNAIso0min
+  GSM84506: 
+    condition: YSHotPhenolRNAIso0min
+:platform: GPL1859

data/install_scripts/GEO/series/GSE3685.yaml

@@ -0,0 +1,31 @@
+--- 
+:title: RNA polymerase II
+:description: |-
+  Determine if increase in transcript abundance was the result of de novo transcription
+  Keywords: Time-course
+:arrays: 
+  GSM84518: 
+    time: YSS288c0min
+  GSM84520: 
+    time: YSS288c30min
+  GSM84519: 
+    time: YSS288c2min
+  GSM84510: 
+    time: YSRNAPolIImut0min
+  GSM84509: 
+    time: YSRNAPolIImut0min
+  GSM84511: 
+    time: YSRNAPolIImut2min
+  GSM84512: 
+    time: YSRNAPolIImut30min
+  GSM84513: 
+    time: YSRNAPolIIpar0min
+  GSM84514: 
+    time: YSRNAPolIIpar0min
+  GSM84515: 
+    time: YSRNAPolIIpar2min
+  GSM84516: 
+    time: YSRNAPolIIpar30min
+  GSM84517: 
+    time: YSS288c0min
+:platform: GPL1859

data/install_scripts/GEO/series/GSE3686.yaml

@@ -0,0 +1,63 @@
+--- 
+:title: Protease Treatment
+:description: |-
+  Determine if transcripts are released by protease treatment
+  Keywords: Comparison of protease treatments
+:arrays: 
+  GSM84540: 
+    condition: Stationary Phase Qiagen Protease treated
+  GSM84529: 
+    condition: Exponential proteinase K treated
+  GSM84541: 
+    condition: Stationary Phase proteinase K treated
+  GSM84530: 
+    condition: Exponential proteinase K treated
+  GSM84542: 
+    condition: Stationary Phase proteinase K treated
+  GSM84531: 
+    condition: Exponential trypsin treated
+  GSM84543: 
+    condition: Stationary Phase trypsin treated
+  GSM84532: 
+    condition: Exponential trypsin treated
+  GSM84521: 
+    condition: Exponential Qiagen Protease Non-treated
+  GSM84544: 
+    condition: Stationary Phase trypsin treated
+  GSM84533: 
+    condition: Stationary Phase Qiagen Protease Non-treated
+  GSM84522: 
+    condition: Exponential Qiagen Protease Non-treated
+  GSM84545: 
+    condition: Stationary Phase trypsin Non-treated time 2 mins
+  GSM84534: 
+    condition: Stationary Phase Qiagen Protease Non-treated
+  GSM84523: 
+    condition: Exponential proteinase K Non-treated
+  GSM84546: 
+    condition: Stationary Phase trypsin Non-treated time 2 mins
+  GSM84535: 
+    condition: Stationary Phase proteinase K Non-treated
+  GSM84524: 
+    condition: Exponential proteinase K Non-treated
+  GSM84547: 
+    condition: Stationary Phase trypsin treated time 2 mins
+  GSM84536: 
+    condition: Stationary Phase proteinase K Non-treated
+  GSM84525: 
+    condition: Exponential trypsin Non-treated
+  GSM84548: 
+    condition: Stationary Phase trypsin treated time 2 mins
+  GSM84537: 
+    condition: Stationary Phase trypsin Non-treated
+  GSM84526: 
+    condition: Exponential trypsin Non-treated
+  GSM84538: 
+    condition: Stationary Phase trypsin Non-treated
+  GSM84527: 
+    condition: Exponential Qiagen Protease treated
+  GSM84539: 
+    condition: Stationary Phase Qiagen Protease treated
+  GSM84528: 
+    condition: Exponential Qiagen Protease treated
+:platform: GPL1859

data/install_scripts/GEO/series/GSE3687.yaml

@@ -0,0 +1,83 @@
+--- 
+:title: Temperature Upshift
+:description: |-
+  Determine if cells in stationary-phase cultures respond to increased temperature.
+  Keywords: Time-course
+:arrays: 
+  GSM84485: 
+    time: "210"
+  GSM84474: 
+    time: "360"
+  GSM84463: 
+    time: "30"
+  GSM84419: 
+    time: "0"
+  GSM84486: 
+    time: "240"
+  GSM84475: 
+    time: "390"
+  GSM84464: 
+    time: "60"
+  GSM84420: 
+    time: "0"
+  GSM84487: 
+    time: "270"
+  GSM84476: 
+    time: "420"
+  GSM84465: 
+    time: "90"
+  GSM84488: 
+    time: "300"
+  GSM84477: 
+    time: "450"
+  GSM84466: 
+    time: "120"
+  GSM84489: 
+    time: "330"
+  GSM84478: 
+    time: "480"
+  GSM84467: 
+    time: "150"
+  GSM84490: 
+    time: "360"
+  GSM84479: 
+    time: "30"
+  GSM84468: 
+    time: "180"
+  GSM84491: 
+    time: "390"
+  GSM84480: 
+    time: "60"
+  GSM84469: 
+    time: "210"
+  GSM84492: 
+    time: "420"
+  GSM84481: 
+    time: "90"
+  GSM84470: 
+    time: "240"
+  GSM84415: 
+    time: "0"
+  GSM84493: 
+    time: "450"
+  GSM84482: 
+    time: "120"
+  GSM84471: 
+    time: "270"
+  GSM84416: 
+    time: "0"
+  GSM84494: 
+    time: "480"
+  GSM84483: 
+    time: "150"
+  GSM84472: 
+    time: "300"
+  GSM84417: 
+    time: "0"
+  GSM84484: 
+    time: "180"
+  GSM84473: 
+    time: "330"
+  GSM84418: 
+    time: "0"
+:platform: GPL3153

data/install_scripts/GEO/series/GSE3802.yaml

@@ -0,0 +1,19 @@
+--- 
+:title: Histone H2B^3-32
+:description: |-
+  Histone H2B was mutated to give H2B^3-32.  Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays.  Comparisons between the sample groups allow the identification of genes regulated by H2B N-terminal domain.
+  Keywords: repeat
+:arrays: 
+  GSM86746: 
+    condition: Wild-type for H2B
+  GSM86747: 
+    condition: Wild-type for H2B
+  GSM86748: 
+    condition: Wild-type for H2B
+  GSM86749: 
+    condition: Mutant Histone H2B
+  GSM86750: 
+    condition: Mutant Histone H2B
+  GSM86751: 
+    condition: Mutant Histone H2B
+:platform: GPL90

data/install_scripts/GEO/series/GSE3803.yaml

@@ -0,0 +1,19 @@
+--- 
+:title: Histone H2B K->G
+:description: |-
+  Histone H2B was mutated to give H2B K6,11,16,17,21,22G.  Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays.  Comparisons between the sample groups allow the identification of genes regulated by H2B N-terminal acetylated lysine residues.
+  Keywords: repeat
+:arrays: 
+  GSM86753: 
+    condition: Wild-type for Histone H2B K->G
+  GSM86755: 
+    condition: Mutant Histone H2B K->G
+  GSM86756: 
+    condition: Mutant Histone H2B K->G
+  GSM86757: 
+    condition: Mutant Histone H2B K->G
+  GSM86748: 
+    condition: Wild-type for Histone H2B K->G
+  GSM86752: 
+    condition: Wild-type for Histone H2B K->G
+:platform: GPL90

data/install_scripts/GEO/series/GSE3804.yaml

@@ -0,0 +1,19 @@
+--- 
+:title: Histone H2B^3-37
+:description: |-
+  Histone H2B was mutated to give H2B^3-37.  Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays.  Comparisons between the sample groups allow the identification of genes regulated by H2B N-terminal domain.
+  Keywords: repeat
+:arrays: 
+  GSM86758: 
+    condition: Wild-type for Histone H2B
+  GSM86759: 
+    condition: Wild-type for Histone H2B
+  GSM86748: 
+    condition: Wild-type for Histone H2B
+  GSM86761: 
+    condition: Mutant Histone H2B
+  GSM86762: 
+    condition: Mutant Histone H2B
+  GSM86763: 
+    condition: Mutant Histone H2B
+:platform: GPL90

data/install_scripts/GEO/series/GSE3805.yaml

@@ -0,0 +1,19 @@
+--- 
+:title: Histone H2B^30-37
+:description: |-
+  Histone H2B was mutated to give H2B^30-37.  Total RNA from three replicate cultures of wild-type and mutant was isolated and the expression profiles were determined using Affymetrix arrays.  Comparisons between the sample groups allow the identification of genes regulated by H2B HBR domain.
+  Keywords: repeat
+:arrays: 
+  GSM86764: 
+    condition: Wild-type for H2B
+  GSM86767: 
+    condition: Mutant Histone H2B
+  GSM86768: 
+    condition: Mutant Histone H2B
+  GSM86769: 
+    condition: Mutant Histone H2B
+  GSM86759: 
+    condition: Wild-type for H2B
+  GSM86748: 
+    condition: Wild-type for H2B
+:platform: GPL90

data/install_scripts/GEO/series/GSE3813.yaml

@@ -0,0 +1,9 @@
+--- 
+:title: Comparision of Total RNA from WT and RRP6delta S. cerevisiae using ORF + Intergenic Array
+:description: |-
+  This data set represents the results of two reverse labeled experiments from wild-type and RRP6delta S. cerevisiae that has been hybed to arrays containing PCR products for ORFs and Intergenic Features
+  Keywords: genetic modification
+:arrays: 
+  GSM86408: 
+    condition: RRP6  vs RRP6-
+:platform: GPL3237

data/install_scripts/GEO/series/GSE3814.yaml

@@ -0,0 +1,71 @@
+--- 
+:title: Sporulation_transfer_to_glucose
+: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
+:arrays: 
+  GSM87543: 
+    condition: RTG_6R40
+  GSM87532: 
+    condition: RTG_3R0
+  GSM87521: 
+    condition: Sporulation_2h
+  GSM87544: 
+    condition: RTG_7R0
+  GSM87533: 
+    condition: RTG_3R20
+  GSM87522: 
+    condition: Sporulation_3h
+  GSM87545: 
+    condition: RTG_7R20
+  GSM87534: 
+    condition: RTG_3R40
+  GSM87523: 
+    condition: Sporulation_4h
+  GSM87546: 
+    condition: RTG_7R40
+  GSM87535: 
+    condition: RTG_4R0
+  GSM87524: 
+    condition: Sporulation_5h
+  GSM87547: 
+    condition: RTG_8R0
+  GSM87536: 
+    condition: RTG_4R20
+  GSM87525: 
+    condition: Sporulation_6h
+  GSM87548: 
+    condition: RTG_8R20
+  GSM87537: 
+    condition: RTG_4R40
+  GSM87526: 
+    condition: Sporulation_7h
+  GSM87549: 
+    condition: RTG_8R40
+  GSM87538: 
+    condition: RTG_5R0
+  GSM87527: 
+    condition: Sporulation_8h
+  GSM87550: 
+    condition: RTG_9R0
+  GSM87539: 
+    condition: RTG_5R20
+  GSM87528: 
+    condition: Sporulation_9h
+  GSM87551: 
+    condition: RTG_9R20
+  GSM87540: 
+    condition: RTG_5R40
+  GSM87529: 
+    condition: RTG_2R0
+  GSM87552: 
+    condition: RTG_9R40
+  GSM87541: 
+    condition: RTG_6R0
+  GSM87530: 
+    condition: RTG_2R20
+  GSM87542: 
+    condition: RTG_6R20
+  GSM87531: 
+    condition: RTG_2R40
+:platform: GPL3245