rbbt-marq 1.0.0

data/install_scripts/GEO/series/GSE4295.yaml

@@ -0,0 +1,63 @@
+--- 
+:arrays: 
+  GSM98279: 
+    condition: 20sugarHS
+  GSM98268: 
+    condition: 30sugarLS
+  GSM98280: 
+    condition: 20sugarHS
+  GSM98269: 
+    condition: 40sugarLS
+  GSM98281: 
+    condition: 30sugarHS
+  GSM98270: 
+    condition: 40sugarLS
+  GSM98259: 
+    condition: 0sugarLS
+  GSM98282: 
+    condition: 30sugarHS
+  GSM98271: 
+    condition: 50sugarLS
+  GSM98260: 
+    condition: 0sugarLS
+  GSM98283: 
+    condition: 40sugarHS
+  GSM98272: 
+    condition: 50sugarLS
+  GSM98261: 
+    condition: 5sugarLS
+  GSM98284: 
+    condition: 40sugarHS
+  GSM98273: 
+    condition: 0sugarHS
+  GSM98262: 
+    condition: 5sugarLS
+  GSM98285: 
+    condition: 50sugarHS
+  GSM98274: 
+    condition: 0sugarHS
+  GSM98263: 
+    condition: 10sugarLS
+  GSM98286: 
+    condition: 50sugarHS
+  GSM98275: 
+    condition: 5sugarHS
+  GSM98264: 
+    condition: 10sugarLS
+  GSM98276: 
+    condition: 5sugarHS
+  GSM98265: 
+    condition: 20sugarLS
+  GSM98277: 
+    condition: 10sugarHS
+  GSM98266: 
+    condition: 20sugarLS
+  GSM98278: 
+    condition: 10sugarHS
+  GSM98267: 
+    condition: 30sugarLS
+:description: |-
+  Functional genomic analysis using different types of baker's yeast.
+  Keywords: fermentation
+:platform: GPL2529
+:title: Sugar stress during fermentation (baker's yeast)

data/install_scripts/GEO/series/GSE4398.yaml

@@ -0,0 +1,50 @@
+--- 
+:arrays: 
+  GSM72035: 
+    condition: 03II01 batch p12
+  GSM72036: 
+    condition: 03II01 batch p4
+  GSM72025: 
+    condition: Low-D chemostat vs. High-D chemostat
+  GSM72037: 
+    condition: 03II01 batch p5
+  GSM72026: 
+    condition: 03II01 batch p6
+  GSM72038: 
+    condition: batch 02X25 6
+  GSM72027: 
+    condition: 03II01 batch p7
+  GSM72039: 
+    condition: batch 02X25 1
+  GSM72028: 
+    condition: 03II01 batch p8
+  GSM72040: 
+    condition: batch 02X25 2
+  GSM72029: 
+    condition: 03II01 batch p9
+  GSM72041: 
+    condition: batch 02X25 3
+  GSM72030: 
+    condition: 03II01 batch p1
+  GSM72042: 
+    condition: batch 02X25 7
+  GSM72031: 
+    condition: 03II01 batch p10
+  GSM72043: 
+    condition: batch 02X25 4
+  GSM72032: 
+    condition: 03II01 batch p2
+  GSM72044: 
+    condition: batch 02X25 5
+  GSM72033: 
+    condition: 03II01 batch p11
+  GSM72034: 
+    condition: 03II01 batch p3
+:description: |-
+  This SuperSeries is composed of the following subset Series:
+  GSE3205: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1
+  GSE3206: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 2
+  Abstract: We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady state in glucose-limited chemostats corresponds most closely with the state of cells in batch cultures just before they undergo this "diauxic shift." Essentially the same pattern was found between chemostats having a fivefold difference in steady-state growth rate (the lower rate approximating that of the second phase respiratory growth rate in batch cultures). Although in both cases the cells in the chemostat consumed most of the glucose, in neither case did they seem to be metabolizing it primarily through respiration. Although there was some indication of a modest oxidative stress response, the chemostat cultures did not exhibit the massive environmental stress response associated with starvation that also is observed, at least in part, during the diauxic shift in batch cultures. We conclude that despite the theoretical possibility of a switch to fully aerobic metabolism of glucose in the chemostat under conditions of glucose scarcity, homeostatic mechanisms are able to carry out metabolic adjustment as if fermentation of the glucose is the preferred option until the glucose is entirely depleted. These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift.
+  Keywords: SuperSeries
+:platform: GPL2638
+:title: Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures

data/install_scripts/GEO/series/GSE4719.yaml

@@ -0,0 +1,76 @@
+--- 
+:description: "The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1\xE2\x80\x9310. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle\xE2\x80\x93regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle\xE2\x80\x93regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is \xE2\x80\x9Chard wired,\xE2\x80\x9D perhaps at the level of DNA sequence.\n\
+  Keywords: FAIRE"
+:platform: GPL3700
+:title: Yeast FAIRE_Cell Cycle Study
+:arrays: 
+  GSM106533: 
+    time: "54"
+  GSM106522: 
+    time: "18"
+  GSM106511: 
+    time: "90"
+  GSM106534: 
+    time: "63"
+  GSM106523: 
+    time: "18"
+  GSM106512: 
+    time: "90"
+  GSM106535: 
+    time: "63"
+  GSM106524: 
+    time: "18"
+  GSM106513: 
+    time: "90"
+  GSM106536: 
+    time: "63"
+  GSM106525: 
+    time: "36"
+  GSM106514: 
+    time: "90"
+  GSM106537: 
+    time: "63"
+  GSM106526: 
+    time: "36"
+  GSM106515: 
+    time: "90"
+  GSM106538: 
+    time: "72"
+  GSM106527: 
+    time: "36"
+  GSM106528: 
+    time: "36"
+  GSM106517: 
+    time: "90"
+  GSM106506: 
+    time: "72"
+  GSM106541: 
+    time: "54"
+  GSM106530: 
+    time: "36"
+  GSM106529: 
+    time: "36"
+  GSM106518: 
+    time: "0"
+  GSM106507: 
+    time: "72"
+  GSM106542: 
+    time: "54"
+  GSM106531: 
+    time: "54"
+  GSM106520: 
+    time: "0"
+  GSM106519: 
+    time: "0"
+  GSM106508: 
+    time: "72"
+  GSM106543: 
+    time: "0"
+  GSM106532: 
+    time: "54"
+  GSM106521: 
+    time: "18"
+  GSM106510: 
+    time: "72"
+  GSM106509: 
+    time: "72"

data/install_scripts/GEO/series/GSE4720.yaml

@@ -0,0 +1,78 @@
+--- 
+:description: "The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1\xE2\x80\x9310. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle\xE2\x80\x93regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle\xE2\x80\x93regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is \xE2\x80\x9Chard wired,\xE2\x80\x9D perhaps at the level of DNA sequence.\n\
+  Keywords: FAIRE"
+:platform: GPL3700
+:title: Yeast FAIRE_testing wild-type and mutant strains
+:arrays: 
+  GSM106577: 
+    mutant: set1
+  GSM106566: 
+    mutant: h2b
+  GSM106555: 
+    mutant: W303
+  GSM106544: 
+    mutant: set2
+  GSM106578: 
+    mutant: set1
+  GSM106567: 
+    mutant: h3
+  GSM106556: 
+    mutant: BY4741
+  GSM106545: 
+    mutant: set2rad6
+  GSM106579: 
+    mutant: set2
+  GSM106568: 
+    mutant: h3
+  GSM106557: 
+    mutant: BY4741
+  GSM106546: 
+    mutant: set2rad6
+  GSM106570: 
+    mutant: h4
+  GSM106569: 
+    mutant: h4
+  GSM106558: 
+    mutant: BY4741
+  GSM106547: 
+    mutant: set3
+  GSM106571: 
+    mutant: hat1
+  GSM106560: 
+    mutant: BY4741
+  GSM106559: 
+    mutant: BY4741
+  GSM106548: 
+    mutant: set3
+  GSM106572: 
+    mutant: hat1
+  GSM106561: 
+    mutant: gcn5
+  GSM106550: 
+    mutant: set4
+  GSM106549: 
+    mutant: set4
+  GSM106573: 
+    mutant: hat2
+  GSM106562: 
+    mutant: gcn5
+  GSM106551: 
+    mutant: set5
+  GSM106574: 
+    mutant: hat2
+  GSM106563: 
+    mutant: h2a
+  GSM106552: 
+    mutant: set5
+  GSM106575: 
+    mutant: HDACs
+  GSM106564: 
+    mutant: h2a
+  GSM106553: 
+    mutant: set6
+  GSM106576: 
+    mutant: HDACs
+  GSM106565: 
+    mutant: h2b
+  GSM106554: 
+    mutant: set6

data/install_scripts/GEO/series/GSE4721.yaml

@@ -0,0 +1,14 @@
+--- 
+:description: "The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1\xE2\x80\x9310. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle\xE2\x80\x93regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle\xE2\x80\x93regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is \xE2\x80\x9Chard wired,\xE2\x80\x9D perhaps at the level of DNA sequence.\n\
+  Keywords: FAIRE"
+:platform: GPL3703
+:title: Yeast FAIRE_BY4741 on Oligo Arrays
+:arrays: 
+  GSM106580: 
+    condition: BY4741
+  GSM106581: 
+    condition: BY4741
+  GSM106582: 
+    condition: BY4741
+  GSM106583: 
+    condition: BY4741

data/install_scripts/GEO/series/GSE4807.yaml

@@ -0,0 +1,67 @@
+--- 
+:description: |-
+  Addition of 3 new arrays made from carbon limited chemostat of CENPK113-7D and 3 new arrays made from aerobic carbon limited chemostat of CENPK113-7D Complmentary data to the data of the serie GSE1723.
+  Keywords: Chemostat-based transcriptome response comparison
+:title: Carbon-limited anaerobic/aerobic growth of S.cerevisiae-New set
+:arrays: 
+  GSM108394: 
+    condition: Aerobic glucose limited
+  GSM29949: 
+    condition: Anaerobic sulfur limited
+  GSM29927: 
+    condition: Aerobic phosphorus limited
+  GSM29939: 
+    condition: Anaerobic nitrogen limited
+  GSM29917: 
+    condition: Aerobic glucose limited
+  GSM29951: 
+    condition: Anaerobic sulfur limited
+  GSM29940: 
+    condition: Anaerobic nitrogen limited
+  GSM29929: 
+    condition: Aerobic sulfur limited
+  GSM29930: 
+    condition: Aerobic sulfur limited
+  GSM29942: 
+    condition: Anaerobic nitrogen limited
+  GSM29920: 
+    condition: Aerobic nitrogen limited
+  GSM29943: 
+    condition: Anaerobic phosphorus limited
+  GSM29932: 
+    condition: Aerobic sulfur limited
+  GSM29921: 
+    condition: Aerobic nitrogen limited
+  GSM29922: 
+    condition: Aerobic nitrogen limited
+  GSM108368: 
+    condition: Anaerobic carbon limited
+  GSM29945: 
+    condition: Anaerobic phosphorus limited
+  GSM29934: 
+    condition: Anaerobic carbon limited
+  GSM29912: 
+    condition: Aerobic glucose limited
+  GSM108369: 
+    condition: Anaerobic carbon limited
+  GSM29946: 
+    condition: Anaerobic phosphorus limited
+  GSM29924: 
+    condition: Aerobic phosphorus limited
+  GSM108392: 
+    condition: Aerobic glucose limited
+  GSM108370: 
+    condition: Anaerobic carbon limited
+  GSM29936: 
+    condition: Anaerobic carbon limited
+  GSM29914: 
+    condition: Aerobic glucose limited
+  GSM108393: 
+    condition: Aerobic glucose limited
+  GSM29948: 
+    condition: Anaerobic sulfur limited
+  GSM29937: 
+    condition: Anaerobic carbon limited
+  GSM29926: 
+    condition: Aerobic phosphorus limited
+:platform: GPL90

data/install_scripts/GEO/series/GSE4826.yaml

@@ -0,0 +1,39 @@
+--- 
+:description: |-
+  Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type
+  Keywords: quadruplicate mutant:WT analysis, with dye-swapping
+:title: set1, H3K4A, set1htz1, set1htz1sir2 transcription profiles
+:arrays: 
+  GSM108899: 
+    mutant: set1htz1
+  GSM108900: 
+    mutant: set1htz1
+  GSM108901: 
+    mutant: set1htz1sir2
+  GSM108902: 
+    mutant: set1htz1sir2
+  GSM108903: 
+    mutant: set1htz1sir2
+  GSM108893: 
+    mutant: set1
+  GSM108904: 
+    mutant: set1htz1sir2
+  GSM108894: 
+    mutant: set1
+  GSM108905: 
+    mutant: H3K4A
+  GSM108895: 
+    mutant: set1
+  GSM108906: 
+    mutant: H3K4A
+  GSM108896: 
+    mutant: set1
+  GSM108907: 
+    mutant: H3K4A
+  GSM108897: 
+    mutant: set1htz1
+  GSM108908: 
+    mutant: H3K4A
+  GSM108898: 
+    mutant: set1htz1
+:platform: GPL3756

data/install_scripts/GEO/series/GSE4934.yaml

@@ -0,0 +1,23 @@
+--- 
+:description: |-
+  Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type
+  Keywords: quadruplicate mutant:WT analysis, with dye-swapping
+:title: set2, set2sir4 transcription profiles
+:arrays: 
+  GSM111165: 
+    condition: set2
+  GSM111167: 
+    condition: set2sir4
+  GSM111169: 
+    condition: set2sir4
+  GSM111172: 
+    condition: set2sir4
+  GSM111173: 
+    condition: set2sir4
+  GSM111162: 
+    condition: set2
+  GSM111163: 
+    condition: set2
+  GSM111164: 
+    condition: set2
+:platform: GPL3819

data/install_scripts/GEO/series/GSE5027.yaml

@@ -0,0 +1,31 @@
+--- 
+:description: |-
+  This experiment compares transcriptomic response of yeast cells to the deletion of Gcr1 to isogenic wild type strains, grown in YEP(3%)R at 23C.  The goal was to identify misregulated target genes and analyze the functional classifications of those targets.
+  Keywords: cell type comparison
+:title: Transcriptome response to gcr1 deletion in raffinose, galactose, and glucose
+:arrays: 
+  GSM113605: 
+    mutant: gcr1 glu
+  GSM113606: 
+    mutant: gcr1 glu
+  GSM113597: 
+    mutant: gcr1 raff
+  GSM113465: 
+    mutant: gcr1 raff
+  GSM113598: 
+    mutant: gcr1 raff
+  GSM113466: 
+    mutant: gcr1 raff
+  GSM113599: 
+    mutant: gcr1 gal
+  GSM113600: 
+    mutant: gcr1 gal
+  GSM113601: 
+    mutant: gcr1 gal
+  GSM113602: 
+    mutant: gcr1 gal
+  GSM113603: 
+    mutant: gcr1 glu
+  GSM113604: 
+    mutant: gcr1 glu
+:platform: GPL2883