rbbt-marq 1.0.0

data/install_scripts/GEO/series/GSE10268.yaml

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+--- 
+:arrays: 
+  GSM259323: 
+    condition: YPS163 vs DBY8268
+  GSM259312: 
+    condition: YJM269 vs DBY8268
+  GSM259301: 
+    condition: Y1 vs DBY8268
+  GSM259290: 
+    condition: M8 vs DBY8268
+  GSM259279: 
+    condition: K1 vs DBY8268
+  GSM259291: 
+    condition: M8 vs DBY8268
+  GSM259280: 
+    condition: K1 vs DBY8268
+  GSM259324: 
+    condition: YPS163 vs DBY8268
+  GSM259313: 
+    condition: YJM269 vs DBY8268
+  GSM259302: 
+    condition: Y1 vs DBY8268
+  GSM259292: 
+    condition: PR vs DBY8268
+  GSM259281: 
+    condition: K1 vs DBY8268
+  GSM259325: 
+    condition: YPS163 vs DBY8268
+  GSM259314: 
+    condition: YJM308 vs DBY8268
+  GSM259303: 
+    condition: Y1 vs DBY8268
+  GSM259293: 
+    condition: PR vs DBY8268
+  GSM259282: 
+    condition: K9 vs DBY8268
+  GSM259326: 
+    condition: YPS163 vs DBY8268
+  GSM259315: 
+    condition: YJM308 vs DBY8268
+  GSM259304: 
+    condition: Y10 vs DBY8268
+  GSM259294: 
+    condition: PR vs DBY8268
+  GSM259283: 
+    condition: K9 vs DBY8268
+  GSM259316: 
+    condition: YJM308 vs DBY8268
+  GSM259305: 
+    condition: Y10 vs DBY8268
+  GSM259295: 
+    condition: RM11a vs DBY8268
+  GSM259284: 
+    condition: K9 vs DBY8268
+  GSM259273: 
+    condition: B1 vs DBY8268
+  GSM259317: 
+    condition: YJM789 vs DBY8268
+  GSM259306: 
+    condition: Y10 vs DBY8268
+  GSM259296: 
+    condition: RM11a vs DBY8268
+  GSM259285: 
+    condition: M22 vs DBY8268
+  GSM259274: 
+    condition: B1 vs DBY8268
+  GSM259318: 
+    condition: YJM789 vs DBY8268
+  GSM259307: 
+    condition: Y10 vs DBY8268
+  GSM259297: 
+    condition: RM11a vs DBY8268
+  GSM259286: 
+    condition: M22 vs DBY8268
+  GSM259275: 
+    condition: B1 vs DBY8268
+  GSM259320: 
+    condition: YPS1009 vs DBY8268
+  GSM259319: 
+    condition: YJM789 vs DBY8268
+  GSM259308: 
+    condition: Y12 vs DBY8268
+  GSM259298: 
+    condition: SB vs DBY8268
+  GSM259287: 
+    condition: M22 vs DBY8268
+  GSM259276: 
+    condition: I14 vs DBY8268
+  GSM259321: 
+    condition: YPS1009 vs DBY8268
+  GSM259310: 
+    condition: Y12 vs DBY8268
+  GSM259309: 
+    condition: Y12 vs DBY8268
+  GSM259299: 
+    condition: SB vs DBY8268
+  GSM259288: 
+    condition: M8 vs DBY8268
+  GSM259277: 
+    condition: I14 vs DBY8268
+  GSM259322: 
+    condition: YPS1009 vs DBY8268
+  GSM259311: 
+    condition: YJM269 vs DBY8268
+  GSM259300: 
+    condition: SB vs DBY8268
+  GSM259289: 
+    condition: M8 vs DBY8268
+  GSM259278: 
+    condition: I14 vs DBY8268
+:description: |-
+  Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain
+  Keywords: Gene expression comparisons in different yeast strains
+:title: Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (CGH)
+:platform: GPL5915

data/install_scripts/GEO/series/GSE10279.yaml

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+--- 
+:arrays: 
+  GSM259466: 
+    condition: Khd1 IP
+  GSM259467: 
+    condition: Khd1 IP
+  GSM259468: 
+    condition: BY4741 mock
+  GSM259462: 
+    condition: BY4741 mock
+  GSM259463: 
+    condition: BY4741 mock
+  GSM259464: 
+    condition: Khd1 IP
+  GSM259465: 
+    condition: BY4741 mock
+:description: |-
+  RNA-coimmunopurifications with TAP-tagged Khd1 protein from Saccharomyces cereviseae. Untagged strain (BY4741) served as a control (Gerber et al., 2004). Cells were grown to midlog phase in rich media and harvested by centrifugation. TAP-tagged Khd1 was affinity purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input) and from purified protein samples by phenol-chloroform extraction. RNAs were reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/ dNTP mixture. cDNAs were fluorescently labeled and hybridized on yeast DNA microarrays over night at 65 degrees. For a detailed procedure see http://microarray-pubs.stanford.edu/yeast_puf and also Gerber AP et al. PLoS Biology, 2004.
+  An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
+  Strain Name: yeast strain with/without TAP-tagged Khd1
+  Keywords: all_pairs
+:title: Khd1p associated mRNAs
+:platform: GPL6419

data/install_scripts/GEO/series/GSE103.yaml

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+--- 
+:arrays: 
+  GSM3029: 
+    treatment: mex67-6 at 37C vs. Mex67 WT at 37C
+  GSM3018: 
+    treatment: mex67-6 at 37C vs. Mex67 WT at 37C
+  GSM3020: 
+    treatment: mex67-6 at 37C vs. Mex67 WT at 37C
+  GSM3019: 
+    treatment: mex67-6 at 37C vs. Mex67 WT at 37C
+  GSM3021: 
+    treatment: mex67-6 at 37C vs. Mex67 WT at 37C
+  GSM3022: 
+    treatment: mex67-6 at 37C vs. Mex67 WT at 37C
+:description: |-
+  Comparison of cDNA from RNA of mex67-5 temperature-sensitive mutant to RNA from Mex67 wildtype strain both at the non-permissive temperature of 37C
+  Keywords: repeat sample
+:title: total RNA from mex67-6 at 37C vs. Mex67 WT at 37C (mex67-5TS_v_Mex67WT)
+:platform: GPL220

data/install_scripts/GEO/series/GSE104.yaml

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+--- 
+:arrays: 
+  GSM3023: 
+    treatment: yra1-1 at 37C vs. Yra1 WT at 37C
+  GSM3024: 
+    treatment: yra1-1 at 37C vs. Yra1 WT at 37C
+  GSM3025: 
+    treatment: yra1-1 at 37C vs. Yra1 WT at 37C
+  GSM3026: 
+    treatment: yra1-1 at 37C vs. Yra1 WT at 37C
+  GSM3027: 
+    treatment: yra1-1 at 37C vs. Yra1 WT at 37C
+  GSM3028: 
+    treatment: yra1-1 at 37C vs. Yra1 WT at 37C
+:description: |-
+  Comparison of cDNA from RNA of yra1-1 temperature-sensitive mutant to RNA from Yra1 wildtype strain both at the non-permissive temperature of 37C
+  Keywords: repeat sample
+:title: total RNA from yra1-1 at 37C vs. Yra1 WT at 37C (yra1-1TS_v_Yra1WT)
+:platform: GPL220

data/install_scripts/GEO/series/GSE10514.yaml

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+--- 
+:arrays: 
+  GSM265792: 
+    treatment: TAP_TAG
+  GSM265781: 
+    treatment: Streptavidin_Aptamer
+  GSM265793: 
+    treatment: Rpr1_ts
+  GSM265782: 
+    treatment: TAP_TAG
+  GSM265794: 
+    treatment: Pop1_ts1
+  GSM265783: 
+    treatment: Rpr1_ts
+  GSM265795: 
+    treatment: Pop1_ts2
+  GSM265784: 
+    treatment: Pop1_ts1
+  GSM265796: 
+    treatment: Streptavidin_Aptamer
+  GSM265785: 
+    treatment: Pop1_ts2
+:description: |-
+  Numerous RNAs copurify with RNase P and are affected by temperture sensitive mutations in conserved residues with the essential RNA and protein subunits.  Specifically, RNase P physically interacts with ribosomal protein mRNAS and the intron-encoded box C/D snoRNAs.
+  Keywords: RNA copurification, temperature sensitive mutants
+:title: Identification of RNAs that are physically and functionally associated with RNase P
+:platform: GPL6424

data/install_scripts/GEO/series/GSE10521.yaml

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+--- 
+:arrays: 
+  GSM265836: 
+    condition: caf130_glu
+  GSM265825: 
+    condition: ccr4
+  GSM265837: 
+    condition: caf130_glu
+  GSM265826: 
+    condition: ccr4
+  GSM265838: 
+    condition: ccr4_glu
+  GSM265827: 
+    condition: not2
+  GSM265839: 
+    condition: ccr4_glu
+  GSM265828: 
+    condition: not2
+  GSM265840: 
+    condition: not2_glu
+  GSM265829: 
+    condition: not3
+  GSM265841: 
+    condition: not2_glu
+  GSM265830: 
+    condition: not3
+  GSM265842: 
+    condition: not4_glu
+  GSM265831: 
+    condition: not4
+  GSM265843: 
+    condition: not4_glu
+  GSM265832: 
+    condition: not5
+  GSM265821: 
+    condition: caf1
+  GSM265844: 
+    condition: wt_glu
+  GSM265833: 
+    condition: wt
+  GSM265822: 
+    condition: caf1
+  GSM265845: 
+    condition: wt_glu
+  GSM265834: 
+    condition: wt
+  GSM265823: 
+    condition: caf130
+  GSM265835: 
+    condition: caf1_glu
+  GSM265824: 
+    condition: caf130
+:description: "These Affymetrix data were used to determine the role of each non-essential subunit of the conserved Ccr4-Not complex in the control of gene expression in the yeast S. cerevisiae. The study was performed with cells growing exponentially in high glucose and with cells grown to glucose depletion. Specific patterns of gene de-regulation were observed upon deletion of any given subunit, revealing the specificity of each subunit\xE2\x80\x99s function. Consistently, the purification of the Ccr4-Not complex through Caf40p by tandem affinity purification from wild-type cells or cells lacking individual subunits of the Ccr4-Not complex revealed that each subunit had a particular impact on complex integrity. Furthermore, the micro-arrays revealed that the role of each subunit was specific to the growth conditions. From the study of only two different growth conditions, revealing an impact of the Ccr4-Not complex on more than 85% of all studied genes, we can infer that the Ccr4-Not complex is important for expression of most of the yeast genome.\n\
+  Keywords: genetic modification, stress response"
+:title: Specific Roles for the Ccr4-Not Complex Subunits in Expression of the Genome
+:platform: GPL90

data/install_scripts/GEO/series/GSE10554.yaml

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+--- 
+:arrays: 
+  GSM266725: 
+    treatment: Ptero_Control
+  GSM266726: 
+    treatment: Ptero_Treated
+  GSM266728: 
+    treatment: Ptero_Treated
+  GSM266729: 
+    treatment: Ptero_Treated
+  GSM266723: 
+    treatment: Ptero_Control
+  GSM266724: 
+    treatment: Ptero_Control
+:description: |-
+  Background:  Pterostilbene, a naturally occurring phenolic compound produced by agronomically important plant genera such as Vitis and Vacciunium, is a phytoalexin exhibiting potent antifungal activity.  Additionally, recent studies have demonstrated several important pharmacological properties associated with pterostilbene.  Despite this, a systematic study of the effects of pterostilbene on eukaryotic cells at the molecular level has not been previously reported.  Thus, the aim of the present study was to identify the cellular pathways affected by pterostilbene by performing transcript profiling studies, employing the model yeast Saccharomyces cerevisiae.  Methods:  S. cerevisiae strain S288C was exposed to pterostilbene at the IC50 concentration (70 uM) for one generation (3 h).  Transcript profiling experiments were performed on three biological replicate samples using the Affymetrix GeneChip Yeast Genome S98 Array.  The data were analyzed using the statistical methods available in the GeneSifter microarray data analysis system.   To validate the results, eleven differentially expressed genes were further examined by quantitative real-time RT-PCR, and S. cerevisiae mutant strains with deletions in these genes were analyzed for altered sensitivity to pterostilbene.  Results: Transcript profiling studies revealed that pterostilbene exposure significantly down-regulated the expression of genes involved in methionine metabolism, while the expression of genes involved in mitochondrial functions, drug detoxification, and transcription factor activity were significantly up-regulated.  Additional analyses revealed that a large number of genes involved in lipid metabolism were also affected by pterostilbene treatment.  Conclusions:  Using transcript profiling, we have identified the cellular pathways targeted by pterostilbene, an analog of resveratrol.  The observed response in lipid metabolism genes is consistent with its known hypolipidemic properties, and the induction of mitochondrial genes is consistent with its demonstrated role in apoptosis in human cancer cell lines. Furthermore, our data show that pterostilbene has a significant effect on methionine metabolism, a previously unreported effect for this compound.
+  Keywords: Transcript profiling, S. cerevisiae, pterostilbene
+:title: Identification of Molecular Pathways Affected by Pterostilbene, a Natural Dimethylether Analog of Resveratrol
+:platform: GPL90

data/install_scripts/GEO/series/GSE1073.yaml

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+--- 
+:arrays: 
+  GSM17187: 
+    condition: M8Rich
+  GSM17176: 
+    condition: S288CRich
+  GSM17165: 
+    condition: M13Rich
+  GSM17154: 
+    condition: M5Cusulf
+  GSM17143: 
+    condition: M34Cusulf
+  GSM17188: 
+    condition: M34Rich
+  GSM17177: 
+    condition: YPS163Rich
+  GSM17166: 
+    condition: M22Rich
+  GSM17155: 
+    condition: M14Cusulf
+  GSM17144: 
+    condition: M32CuSulf
+  GSM17189: 
+    condition: Ref
+  GSM17178: 
+    condition: M8Rich
+  GSM17167: 
+    condition: S288CRich
+  GSM17156: 
+    condition: M13Cusulf
+  GSM17145: 
+    condition: M5Cusulf
+  GSM17190: 
+    condition: Ref
+  GSM17179: 
+    condition: M34Rich
+  GSM17168: 
+    condition: YPS163Rich
+  GSM17157: 
+    condition: M22Cusulf
+  GSM17146: 
+    condition: M14Cusulf
+  GSM17135: 
+    condition: M32CuSulf
+  GSM17191: 
+    condition: Ref
+  GSM17180: 
+    condition: M32Rich
+  GSM17169: 
+    condition: M8Rich
+  GSM17158: 
+    condition: S288CCusulf
+  GSM17147: 
+    condition: M13Cusulf
+  GSM17136: 
+    condition: M5Cusulf
+  GSM17192: 
+    condition: Ref
+  GSM17181: 
+    condition: M5Rich
+  GSM17170: 
+    condition: M34Rich
+  GSM17159: 
+    condition: YPS163Cusulf
+  GSM17148: 
+    condition: M22Cusulf
+  GSM17137: 
+    condition: M14Cusulf
+  GSM17193: 
+    condition: Ref
+  GSM17182: 
+    condition: M14Rich
+  GSM17171: 
+    condition: M32Rich
+  GSM17160: 
+    condition: M8Cusulf
+  GSM17149: 
+    condition: S288CCusulf
+  GSM17138: 
+    condition: M13Cusulf
+  GSM17194: 
+    condition: Ref
+  GSM17183: 
+    condition: M13Rich
+  GSM17172: 
+    condition: M5Rich
+  GSM17161: 
+    condition: M34Cusulf
+  GSM17150: 
+    condition: YPS163Cusulf
+  GSM17139: 
+    condition: M22Cusulf
+  GSM17184: 
+    condition: M22Rich
+  GSM17173: 
+    condition: M14Rich
+  GSM17162: 
+    condition: M32Rich
+  GSM17151: 
+    condition: M8Cusulf
+  GSM17140: 
+    condition: S288CCusulf
+  GSM17185: 
+    condition: S288CRich
+  GSM17174: 
+    condition: M13Rich
+  GSM17163: 
+    condition: M5Rich
+  GSM17152: 
+    condition: M34Cusulf
+  GSM17141: 
+    condition: YPS163Cusulf
+  GSM17186: 
+    condition: YPS163Rich
+  GSM17175: 
+    condition: M22Rich
+  GSM17164: 
+    condition: M14Rich
+  GSM17153: 
+    condition: M32Cusulf
+  GSM17142: 
+    condition: M8Cusulf
+:description: |-
+  Each strain was grown overnight then diluted in fresh rich media. After three hours strains were again rediluted into either rich media or rich media supplemented with copper sulfate. After another three hours cultures were sampled, cells lysed and flash frozen using liquid nitrogen. RNA was extrated using hot phenol-chloroform, reverse transcripbed using amino-allyle dUTP and labelled with either Cy3 or Cy5 flourescent dye. Each hybridization is of a single sample compared to a reference pool contructed from all the strains with the same treatment. Labelled probe were hybridized to DNA microarrays spotted with 6144 70 bp oligonucleotides obtained from Qiagen-Operon. After an overnight hybridization, microarrays were scanned using a GenePix 4000A scanner and spot intensities extracted using GenePix 4.0 software. Bad spots were flagged based on the image.
+  Keywords: other
+:title: Strain differences in copper sulfate
+:platform: GPL1007

data/install_scripts/GEO/series/GSE10860.yaml

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+--- 
+:arrays: 
+  GSM275454: 
+    condition: H4 alleles
+  GSM275455: 
+    condition: H4 alleles
+  GSM275456: 
+    condition: H3/H4 alleles-10d
+  GSM275457: 
+    condition: H3/H4 alleles-10d
+  GSM275458: 
+    condition: ChemostH3/H4 alleles-20dat growth of histone H3/H4 alleles, day 20
+  GSM275460: 
+    condition: slt2vsH3/H4
+  GSM275459: 
+    condition: over-represented histone alleles-10d
+  GSM275461: 
+    condition: slt2vsH3/H4
+  GSM275462: 
+    condition: H3/H4 alleles end-j
+:description: |-
+  The structural integrity of the nucleosome is central to regulation of DNA metabolism and transcription. We describe a library of 486 systematic histone H3 and H4 substitution and deletion mutants in Saccharomyces cerevisiae that probe the contribution of each residue to nucleosome function and can be episomal or genomically integrated. We tagged each mutant histone gene with unique molecular barcodes, facilitating identification of mutant pools through barcode amplification, labeling, and microarray hybridization. We probed fitness contributions of each residue to chemical perturbagens of chromosome integrity and transcription, mapping global patterns of chemical sensitivities and requirements for three forms of transcriptional silencing onto the nucleosome surface. Lethal mutants were surprisingly rare and of distinct types; one set of mutations mapped precisely to the DNA interaction surface. The barcode microarrays were useful for scoring complex phenotypes such as competitive fitness in a chemostat, proficiency of DNA repair, and synthetic genetic interactions.
+  Keywords: genetic modification
+:title: "Probing nucleosome function: A highly versatile library of synthetic histone H3 and H4 mutants"
+:platform: GPL6574

data/install_scripts/GEO/series/GSE10930.yaml

@@ -0,0 +1,15 @@
+--- 
+:arrays: 
+  GSM277242: 
+    condition: wt
+  GSM277243: 
+    condition: wt
+  GSM277244: 
+    condition: H3mut
+  GSM277245: 
+    condition: h3mut
+:description: |-
+  Total RNA from two replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by histone H3 K4,36,79G mutant.
+  Keywords: repeat
+:title: Histone H3 K4,36,79G
+:platform: GPL90