rbbt-marq 1.0.0

data/install_scripts/GEO/platforms/GPL92.yaml

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+--- 
+:title: Affymetrix GeneChip Human Genome U95 Set HG-U95B
+:BioMart_ID: AFFY HG U95B
+:organism: human

data/install_scripts/GEO/platforms/GPL920.yaml

@@ -0,0 +1,7 @@
+--- 
+:other_ID_field: 
+- 2
+- GENE_LIST
+:title: yeast32canada
+:organism: sgd
+:BioMart_ID: 

data/install_scripts/GEO/platforms/GPL922.yaml

@@ -0,0 +1,7 @@
+--- 
+:title: Agilent-011472 Mouse Development Oligo Microarray G4120A (Feature Number version)
+:BioMart_ID: 
+:other_ID_field: 
+- 7
+- GB_ACC
+:organism: mgi

data/install_scripts/GEO/platforms/GPL924.yaml

@@ -0,0 +1,7 @@
+--- 
+:title: UCSF elegans_mod 19K array
+:BioMart_ID: 
+:other_ID_field: 
+- 3
+- ORF
+:organism: worm

data/install_scripts/GEO/platforms/GPL93.yaml

@@ -0,0 +1,4 @@
+--- 
+:title: Affymetrix GeneChip Human Genome U95 Set HG-U95C
+:BioMart_ID: AFFY HG U95C
+:organism: human

data/install_scripts/GEO/platforms/GPL96.yaml

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+--- 
+:title: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A
+:BioMart_ID: AFFY HG U133A
+:organism: human

data/install_scripts/GEO/platforms/GPL968.yaml

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+--- 
+:title: RAT_6K_OligoArray
+:BioMart_ID: 
+:organism: rgd

data/install_scripts/GEO/platforms/GPL97.yaml

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+--- 
+:title: Affymetrix GeneChip Human Genome U133 Array Set HG-U133B
+:BioMart_ID: AFFY HG U133-PLUS-2
+:organism: human

data/install_scripts/GEO/platforms/GPL98.yaml

@@ -0,0 +1,7 @@
+--- 
+:title: Affymetrix GeneChip Human 35K SubA Array Hu35k-A
+:BioMart_ID: 
+:other_ID_field: 
+- 10
+- ENTREZ_GENE_ID
+:organism: human

data/install_scripts/GEO/platforms/GPL981.yaml

@@ -0,0 +1,7 @@
+--- 
+:title: HUMAN_21K_OligoArray_1
+:BioMart_ID: 
+:other_ID_field: 
+- 2
+- BLOCK
+:organism: human

data/install_scripts/GEO/platforms/GPL99.yaml

@@ -0,0 +1,7 @@
+--- 
+:title: Affymetrix GeneChip Human 35K SubB Array Hu35k-B
+:BioMart_ID: 
+:other_ID_field: 
+- 10
+- ENTREZ_GENE_ID
+:organism: human

data/install_scripts/GEO/platforms/GPL999.yaml

@@ -0,0 +1,7 @@
+--- 
+:title: Leber et al. (2004)
+:BioMart_ID: 
+:other_ID_field: 
+- 3
+- GENE
+:organism: sgd

data/install_scripts/GEO/series/GSE10018.yaml

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+--- 
+:arrays: 
+  GSM253185: 
+    generation: Yeast aging 18-20
+  GSM253186: 
+    generation: Yeast aging 18-20
+  GSM253175: 
+    generation: Yeast aging 12
+  GSM253187: 
+    generation: Yeast aging 18-20
+  GSM253176: 
+    generation: Yeast aging 12
+  GSM253188: 
+    generation: Yeast aging 8
+  GSM253177: 
+    generation: Yeast aging 12
+  GSM253190: 
+    generation: Yeast aging 8
+  GSM253189: 
+    generation: Yeast aging 8
+  GSM253178: 
+    generation: Yeast aging 12
+  GSM253167: 
+    generation: Yeast aging 1
+  GSM260329: 
+    generation: Yeast aging 12
+  GSM253191: 
+    generation: Yeast aging 8
+  GSM253180: 
+    generation: Yeast aging 12
+  GSM253179: 
+    generation: Yeast aging 12
+  GSM253168: 
+    generation: Yeast aging 1
+  GSM252981: 
+    generation: Yeast aging 1
+  GSM253192: 
+    generation: Yeast aging 8
+  GSM253181: 
+    generation: Yeast aging 18-20
+  GSM253170: 
+    generation: Yeast aging 1
+  GSM253169: 
+    generation: Yeast aging 1
+  GSM253182: 
+    generation: Yeast aging 18-20
+  GSM253171: 
+    generation: Yeast aging 1
+  GSM260354: 
+    generation: Yeast aging 8
+  GSM253183: 
+    generation: Yeast aging 18-20
+  GSM253172: 
+    generation: Yeast aging 1
+  GSM253184: 
+    generation: Yeast aging 18-20
+:description: |-
+  Yeast replicative aging is a process resembling replicative aging in mammalian cells.  During aging, wild type haploid yeast cells enlarge, become sterile, and undergo nucleolar enlargement and fragmentation; we sought gene expression changes during the time of these phenotypic changes.   Gene expression studied via microarrays and qPCR has shown reproducible, statistically significant changes in mRNA of genes at 12 and 18-20 generations.  Our findings support previously described changes towards aerobic metabolism, decreased ribosome gene expression, and a partial Environmental Stress Response.  Our novel findings include a pseudo-stationary phase, down-regulation of methylation-related metabolism, increased Nucleotide Excision Repair related mRNA, and a strong up-regulation of many of the regulatory subunits of protein phosphatase I (Glc7).  These findings are correlated with aging changes in higher organisms as well as with the known involvement of protein phosphorylation states during yeast aging.  J Gerontol, Jan, 2008, vol 63A, no. 1.
+  Keywords: aging time course
+:title: Pathways change in expression during replicative aging in Saccharomyces cerevisiae
+:platform: GPL5947

data/install_scripts/GEO/series/GSE1002.yaml

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+--- 
+:arrays: 
+  GSM15352: 
+    time: "0"
+    treatment: genomic F6
+  GSM15341: 
+    time: "0"
+    treatment: genomic F1
+  GSM15319: 
+    time: "1"
+    treatment: mRNA
+  GSM15308: 
+    time: "1"
+    treatment: mRNA
+  GSM15297: 
+    time: "2"
+    treatment: GRO
+  GSM15286: 
+    time: "3"
+    treatment: GRO
+  GSM15298: 
+    time: "3"
+    treatment: GRO
+  GSM15287: 
+    time: "4"
+    treatment: GRO
+  GSM15343: 
+    time: "0"
+    treatment: genomic F2
+  GSM15310: 
+    time: "2"
+    treatment: mRNA
+  GSM15299: 
+    time: "4"
+    treatment: GRO
+  GSM15288: 
+    time: "5"
+    treatment: GRO
+  GSM15322: 
+    time: "2"
+    treatment: mRNA
+  GSM15311: 
+    time: "3"
+    treatment: mRNA
+  GSM15300: 
+    time: "5"
+    treatment: GRO
+  GSM15289: 
+    time: "0"
+    treatment: GRO
+  GSM15345: 
+    time: "0"
+    treatment: genomic F3
+  GSM15301: 
+    time: "0"
+    treatment: mRNA
+  GSM15290: 
+    time: "1"
+    treatment: GRO
+  GSM15324: 
+    time: "3"
+    treatment: mRNA
+  GSM15313: 
+    time: "4"
+    treatment: mRNA
+  GSM15302: 
+    time: "1"
+    treatment: mRNA
+  GSM15291: 
+    time: "2"
+    treatment: GRO
+  GSM15347: 
+    time: "0"
+    treatment: genomic F4
+  GSM15303: 
+    time: "2"
+    treatment: mRNA
+  GSM15292: 
+    time: "3"
+    treatment: GRO
+  GSM15326: 
+    time: "4"
+    treatment: mRNA
+  GSM15315: 
+    time: "5"
+    treatment: mRNA
+  GSM15304: 
+    time: "3"
+    treatment: mRNA
+  GSM15293: 
+    time: "4"
+    treatment: GRO
+  GSM15282: 
+    time: "0"
+    treatment: GRO
+  GSM15305: 
+    time: "4"
+    treatment: mRNA
+  GSM15294: 
+    time: "5"
+    treatment: GRO
+  GSM15328: 
+    time: "5"
+    treatment: mRNA
+  GSM15317: 
+    time: "0"
+    treatment: mRNA
+  GSM15306: 
+    time: "5"
+    treatment: mRNA
+  GSM15295: 
+    time: "0"
+    treatment: GRO
+  GSM15284: 
+    time: "1"
+    treatment: GRO
+  GSM15351: 
+    time: "0"
+    treatment: genomic F5
+  GSM15307: 
+    time: "0"
+    treatment: mRNA
+  GSM15296: 
+    time: "1"
+    treatment: GRO
+  GSM15285: 
+    time: "2"
+    treatment: GRO
+:description: |-
+  Timecourse analyses (0 to 850 min) of exponentially growing BQS252 yeast after shift from YPD to YPGal galactose medium.
+  Total RNA in vivo labeled by run-on, or cDNA labelling using random decamers included.
+  Genomic DNA also examined.
+  Keywords: other
+:title: YPD to YPGal timecourse
+:platform: GPL772

data/install_scripts/GEO/series/GSE10066.yaml

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+--- 
+:arrays: 
+  GSM254436: 
+    treatment: C-lim anaerobic 500 mM lactic acid (pH 3)
+  GSM137498: 
+    treatment: C-lim Anaerobic reference (pH 5)
+  GSM254438: 
+    treatment: C-lim anaerobic 500 mM lactic acid (pH 3)
+  GSM137675: 
+    treatment: C-lim Anaerobic reference (pH 5)
+  GSM254443: 
+    treatment: C-lim anaerobic 500 mM lactic acid (pH 3)
+  GSM254444: 
+    treatment: C-lim anaerobic 900 mM lactic acid (pH 5)
+  GSM254433: 
+    treatment: C-lim Anaerobic reference (pH 3)
+  GSM254445: 
+    treatment: C-lim anaerobic 900 mM lactic acid (pH 5)
+  GSM254434: 
+    treatment: C-lim Anaerobic reference (pH 3)
+  GSM254446: 
+    treatment: C-lim anaerobic 900 mM lactic acid (pH 5)
+  GSM254435: 
+    treatment: C-lim Anaerobic reference (pH 3)
+  GSM137497: 
+    treatment: C-lim Anaerobic reference (pH 5)
+:description: |-
+  Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with lactic acid at pH 3 and pH 5.
+  Keywords: response to lactic acid
+:title: Transcriptional responses to lactic acid in anaerobic chemostat cultures of Saccharomyces cerevisiae
+:platform: GPL90

data/install_scripts/GEO/series/GSE10073.yaml

@@ -0,0 +1,19 @@
+--- 
+:arrays: 
+  GSM254768: 
+    treatment: SMP Control
+  GSM254769: 
+    treatment: SMP Control
+  GSM254770: 
+    treatment: SMP Control
+  GSM254771: 
+    treatment: SMP Treated
+  GSM254772: 
+    treatment: SMP Treated
+  GSM254773: 
+    treatment: SMP Treated
+:description: |-
+  Sampangine, a plant-derived alkaloid found in the Annonaceae family, exhibits strong inhibitory activity against the opportunistic fungal pathogens Candida albicans, Cryptococcus neoformans and Aspergillus fumigatus.  In the present study, transcriptional profiling experiments coupled with the analysis of mutants were performed in an effort to elucidate its mechanism of action.  Using Saccharomyces cerevisiae as a model organism, we show that sampangine produces a transcriptional response indicative of hypoxia, altering the expression of genes known to respond to low oxygen conditions.  Several additional lines of evidence obtained suggest that these responses could involve effects on heme.   First, the hem1 deletion mutant lacking the first enzyme in the heme biosynthetic pathway showed increased sensitivity to sampangine, and exogenously supplied hemin partially rescued the inhibitory activity of sampangine in wild-type cells.  In addition, heterozygous mutants with deletions in genes involved in five out of eight steps in the heme biosynthetic pathway showed increased susceptibility to sampangine.  Furthermore, spectral analysis of pyridine extracts indicated significant accumulation of free porphyrins in sampangine-treated cells.  Transcriptional profiling experiments were also performed in C. albicans to investigate the response of a pathogenic fungal species to sampangine.  Taking into account the known differences in the physiological responses of C. albicans and S. cerevisiae to low oxygen, significant correlations were observed between the two transcription profiles suggestive of heme-related defects.  Our results indicate that the antifungal activity of the plant alkaloid sampangine is due, at least in part, to perturbations in the biosynthesis or metabolism of heme.
+  Keywords: antifungal compound, transcriptional profiling, S. cerevisiae
+:title: Gene expression response to the antifungal compound sampangine in S. cerevisiae
+:platform: GPL90

data/install_scripts/GEO/series/GSE10091.yaml

@@ -0,0 +1,15 @@
+--- 
+:arrays: 
+  GSM254979: 
+    treatment: control cells_sub-polysomal
+  GSM254980: 
+    treatment: control cells_polysomal
+  GSM254981: 
+    treatment: DTT-treated cells_sub-polysomal
+  GSM254982: 
+    treatment: DTT-treated cells_polysomal
+:description: |-
+  The accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER) causes stress and induces the unfolded protein response (UPR) which is characterised in part by the transcriptional induction of genes involved in assisting protein folding. Translational responses to ER stress have been less well described and here we report on a genome-wide analysis of translational regulation in the response to the ER stress-inducing agent dithiothreitol (DTT) in Saccharomyces cerevisiae. Although the observed polysome profiles were similar under control and ER stress conditions microarray analysis identified transcipt-specific translational regulation. Genes with functions in ribosomal biogenesis and assembly were translationally repressed under ER stress. In contrast mRNAs for known UPR genes, including the UPR transcription factor HAC1, the ER-oxidoreductase ERO1 and the ER-associated protein degradation (ERAD) gene DER1 were enriched in polysomal fractions under ER stress conditions. In addition, we show that splicing of HAC1 mRNA is required for efficient ribosomal loading and that Gcn2p is required for normal HAC1 splicing, so shedding light on the role of this protein kinase in the UPR pathway.
+  Keywords: stress response, translational analysis
+:title: Transcript-specific translational regulation in the unfolded protein response of Saccharomyces cerevisiae
+:platform: GPL90

data/install_scripts/GEO/series/GSE101.yaml

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+--- 
+:arrays: 
+  GSM3012: 
+    treatment: zzYra1IP_v_TotalRNA
+  GSM3008: 
+    treatment: zzYra1IP_v_TotalRNA
+  GSM3010: 
+    treatment: zzYra1IP_v_TotalRNA
+  GSM3009: 
+    treatment: zzYra1IP_v_TotalRNA
+  GSM3011: 
+    treatment: zzYra1IP_v_TotalRNA
+:description: |-
+  Comparison of cDNA from RNA IPed with zzYra1 to that from total RNA; resulting analysis gives Yra1 binding level relative to total abundance for each mRNA
+  Keywords: repeat sample
+:title: zzYra1 co-IPed RNA vs. Total RNA  (zzYra1IP_v_TotalRNA)
+:platform: GPL220

data/install_scripts/GEO/series/GSE10100.yaml

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+--- 
+:arrays: 
+  GSM240513: 
+    treatment: 1162-65-8 Aflatoxin B1
+  GSM240514: 
+    treatment: 1162-65-8 Aflatoxin B1
+  GSM240515: 
+    treatment: 1162-65-8 Aflatoxin B1
+  GSM240516: 
+    treatment: 1162-65-8 Aflatoxin B1
+:description: "The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous\n\
+  benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. A lethal effect of a certain kind of mycotoxin is weak to yeast. The amount of exposure to yeast used the maximum dissolution density for afratoxin B1 (CAS; 1162-65-8) (10000 ppm, IC80\xEF\xBC\x89. Because the data that was able to be trusted was not obtained, it is not possible to have analyzed toxicity.\n\
+  Keywords: stress response"
+:title: Aflatoxin B1 treatment with 10,000 ppm for 2 h
+:platform: GPL1945

data/install_scripts/GEO/series/GSE10101.yaml

@@ -0,0 +1,15 @@
+--- 
+:arrays: 
+  GSM240517: 
+    treatment: 1165-39-5 Aflatoxin G1
+  GSM240518: 
+    treatment: 1165-39-5 Aflatoxin G1
+  GSM240519: 
+    treatment: 1165-39-5 Aflatoxin G11165-39-5 Aflatoxin G1
+  GSM240520: 
+    treatment: 1165-39-5 Aflatoxin G1
+:description: "The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous\n\
+  benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. A lethal effect of a certain kind of mycotoxin is weak to yeast. The amount of exposure to yeast used the maximum dissolution density for afratoxin G1 (CAS; 1165-39-5) \xEF\xBC\x8810,000 ppm, IC70\xEF\xBC\x89. Because the data that was able to be trusted was not obtained, it is not possible to have analyzed toxicity.\n\
+  Keywords: stress response"
+:title: Aflatoxin G1 treatment with 10,000 ppm for 2 h
+:platform: GPL1945

data/install_scripts/GEO/series/GSE10102.yaml

@@ -0,0 +1,15 @@
+--- 
+:arrays: 
+  GSM240521: 
+    treatment: 51481-10-8 Deoxynivalenol
+  GSM240522: 
+    treatment: 51481-10-8 Deoxynivalenol
+  GSM240523: 
+    treatment: 51481-10-8 Deoxynivalenol 51481-10-8 Deoxynivalenol
+  GSM240524: 
+    treatment: 51481-10-8 Deoxynivalenol
+:description: "The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly. While these industrial chemicals provide numerous\n\
+  benefits, there is no doubt that some have potential to damage the environment and health. Toxicity must be evaluated and use must be carefully controlled and monitored in order to minimize potential damage. DNA microarray technology has become an important new technique in toxicology. We are using the yeast Saccharomyces cerevisiae as a model organism for toxicological study because it is a simple, fast-growing eukaryote that has been thoroughly characterized. In order to evaluate toxicity by newly synthesized or mixture chemicals, toxicity-induced gene expression alteration profiles by known chemicals should be collected. A lethal effect of a certain kind of mycotoxin is weak to yeast. The amount of exposure to yeast used the maximum dissolution density for afratoxin DON (Deoxynivalenol, CAS; 51481-10-8) (10,000 ppm, IC70\xEF\xBC\x89. Because the data that was able to be trusted was not obtained, it is not possible to have analyzed toxicity.\n\
+  Keywords: stress response"
+:title: Deoxynivalenol treatment with 10,000 ppm for 2 h
+:platform: GPL1945

data/install_scripts/GEO/series/GSE10267.yaml

@@ -0,0 +1,37 @@
+--- 
+:arrays: 
+  GSM259268: 
+    condition: Y10 vs DBY8268
+  GSM259270: 
+    condition: YJM789 vs DBY8268
+  GSM259269: 
+    condition: YJM789 vs DBY8268
+  GSM259258: 
+    condition: DBY8268 vs DBY8268
+  GSM259271: 
+    condition: YPS1009 vs DBY8268
+  GSM259260: 
+    condition: DBY8268 vs DBY8268
+  GSM259259: 
+    condition: DBY8268 vs DBY8268
+  GSM259272: 
+    condition: YPS1009 vs DBY8268
+  GSM259261: 
+    condition: K9 vs DBY8268
+  GSM259262: 
+    condition: K9 vs DBY8268
+  GSM259263: 
+    condition: M22 vs DBY8268
+  GSM259264: 
+    condition: M22 vs DBY8268
+  GSM259265: 
+    condition: RM11-1a vs DBY8268
+  GSM259266: 
+    condition: RM11-1a vs DBY8268
+  GSM259267: 
+    condition: Y10 vs DBY8268
+:description: |-
+  Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain
+  Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains
+:title: Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (gene expression)
+:platform: GPL5915