rbbt-marq 1.0.0

data/install_scripts/GEO/series/GSE1553.yaml

@@ -0,0 +1,23 @@
+--- 
+:title: Steady state +/- Gly
+:arrays: 
+  GSM26650: 
+    condition: BY4741-Gly
+  GSM26651: 
+    condition: BY4741-Gly
+  GSM26652: 
+    condition: Y02669-Gly
+  GSM26653: 
+    condition: Y00249-Gly
+  GSM26654: 
+    condition: Y03803-Gly
+  GSM26655: 
+    condition: BY4741-Gly
+  GSM26656: 
+    condition: Y06015-Gly
+  GSM26657: 
+    condition: Y06015-Gly
+:description: |-
+  Cells were grown to early log phase (OD600 ~ 0.2) at 30oC in 1 liter of minimal B medium (Cherest, H., and Surdin-Kerjan, Y. (1992) Genetics 130, 51-58) with or without supplementation with 10 mM glycine and harvested. All cells were harvested by rapid centrifugation at room temperature then flash frozen in liquid nitrogen. Arrays compared expression of Gly- cells to the Gly+ controls. Strain BY4741 was the wild type and several deletion strains were also used.
+  Keywords: parallel sample
+:platform: GPL1336

data/install_scripts/GEO/series/GSE1617.yaml

@@ -0,0 +1,39 @@
+--- 
+:title: Effects of antimitotic drug benomyl on wild-type strain and strains with Yap1 or Pdr1 deletions
+:description: |-
+  Time-course analyses of the modifications of the yeast gene expression program which immediately follows addition of the antimitotic drug benomyl. Parallel experiments were conducted in different genetic contexts using strains deleted in the Yap1 and Pdr1 genes.
+  Keywords: other
+:arrays: 
+  GSM27560: 
+    mutant: WT 40min
+  GSM27561: 
+    mutant: YAP1 0.5min
+  GSM27562: 
+    mutant: YAP1 2min
+  GSM27563: 
+    mutant: YAP1 4min
+  GSM27564: 
+    mutant: YAP1 10min
+  GSM27565: 
+    mutant: YAP1 20min
+  GSM27566: 
+    mutant: PDR1 0.5min
+  GSM27555: 
+    mutant: WT 0.5min
+  GSM27567: 
+    mutant: PDR1 2min
+  GSM27556: 
+    mutant: WT 2min
+  GSM27568: 
+    mutant: PDR1 4min
+  GSM27557: 
+    mutant: WT 4min
+  GSM27569: 
+    mutant: PDR1 10min
+  GSM27558: 
+    mutant: WT 10min
+  GSM27570: 
+    mutant: PDR1 20min
+  GSM27559: 
+    mutant: WT 20min
+:platform: GPL1383

data/install_scripts/GEO/series/GSE1688.yaml

@@ -0,0 +1,36 @@
+--- 
+:title: Unfolded protein response in wildtype, ire1, gcn4, gcn2
+:description: |-
+  We measured steady-state mRNA levels by microarray hybridization, comparing WT, (delta)ire1, (delta)gcn4, and (delta)gcn2 cells treated with 2 mM DTT for 30 min (by which time the UPR is qualitatively complete) to untreated samples of the same genotype. WT cells were taken as a positive control for UPR induction, and (delta)ire1 cells as a negative control. Fold change in expression of a given gene was computed as the ratio of mRNA level in the treated sample to the level in an untreated sample of the same genotype. Values reported here are the log2 fold change.
+  Keywords = unfolded protein response
+  Keywords = UPR
+  Keywords = ire1
+  Keywords = gcn4
+  Keywords = gcn2
+  Keywords: parallel sample
+:arrays: 
+  GSM29047: 
+    tratment: gcn4 DTT vs. gcn4
+  GSM29048: 
+    tratment: gcn4 DTT vs. gcn4
+  GSM29049: 
+    tratment: gcn4 DTT vs. gcn4
+  GSM29050: 
+    tratment: gcn2 DTT vs. gcn2
+  GSM29051: 
+    tratment: gcn2 DTT vs. gcn2
+  GSM29052: 
+    tratment: gcn2 DTT vs. gcn2
+  GSM16985: 
+    tratment: wt DTT vs wt
+  GSM16986: 
+    tratment: wt DTT vs wt
+  GSM29045: 
+    tratment: ire1 DTT vs. ire1
+  GSM16987: 
+    tratment: wt DTT vs wt
+  GSM29046: 
+    tratment: ire1 DTT vs. ire1
+  GSM16988: 
+    tratment: ire1 DTT vs. ire1
+:platform: GPL1001

data/install_scripts/GEO/series/GSE1693.yaml

@@ -0,0 +1,60 @@
+--- 
+:title: A novel response to microtubule perturbation in meiosis
+:description: |-
+  Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30C. Cells were washed with sterilized water the next day and re-suspended in SPII medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 to induce sporulation. Cells were sporulated at room temperature or 30C as indicated. Sporulation medium containing benomyl was always prepared freshly on the day of the experiment following the directions in {Shonn, 2000 #90}. Briefly, DMSO (dimethyl sulfoxide, Sigma-Aldrich) or benomyl [Methyl 1-(butylcarbamoyl)-2-benzimidazolecarbamate, Sigma-Aldrich; 30 mg/ml stock in DMSO] was dissolved in near-boiling SPII medium to avoid precipitation. The medium was then allowed to slowly cool to 30C or room temperature. At the time of drug treatment, cells were filtered and immediately re-suspended in the medium containing benomyl or DMSO.
+  Keywords = benomyl sporulation saccharomyces microtubule spindle checkpoint
+  Keywords: ordered
+:arrays: 
+  GSM35975: 
+    condition: SR5
+  GSM29080: 
+    condition: SD5
+  GSM35976: 
+    condition: SR8
+  GSM35977: 
+    condition: SR8
+  GSM29104: 
+    condition: SF5
+  GSM34889: 
+    condition: SC5
+  GSM29105: 
+    condition: SP4
+  GSM29094: 
+    condition: SB5
+  GSM29083: 
+    condition: SD5
+  GSM34890: 
+    condition: SC5
+  GSM29106: 
+    condition: SP4
+  GSM29073: 
+    condition: SD8
+  GSM34891: 
+    condition: SC8
+  GSM29107: 
+    condition: YPA
+  GSM34892: 
+    condition: SC8
+  GSM29108: 
+    condition: YPA
+  GSM29086: 
+    condition: SB8
+  GSM29109: 
+    condition: YPD
+  GSM29098: 
+    condition: SB5
+  GSM35972: 
+    condition: SR4
+  GSM29110: 
+    condition: YPD
+  GSM29077: 
+    condition: SD8
+  GSM35973: 
+    condition: SR4
+  GSM29089: 
+    condition: SB8
+  GSM35974: 
+    condition: SR5
+  GSM29101: 
+    condition: SF5
+:platform: GPL90

data/install_scripts/GEO/series/GSE1752.yaml

@@ -0,0 +1,32 @@
+--- 
+:title: Benomyl dose-response
+:description: |-
+  Synthetic lethality of Yeast Deletion strain mutations in haploid cells with various concentrations of Benomyl
+  Keywords = Benomyl
+  Keywords = yeast
+  Keywords = deletion
+  Keywords = tag
+  Keywords = barcode
+  Keywords: dose response
+:arrays: 
+  GSM30552: 
+    condition: 10mg/ml benomyl/-benomyl
+  GSM30553: 
+    condition: 15mg/ml benomyl/-benomyl
+  GSM30554: 
+    condition: 20mg/ml benomyl/-benomyl
+  GSM30555: 
+    condition: 25mg/ml benomyl/-benomyl
+  GSM30556: 
+    condition: 30mg/ml benomyl/-benomyl
+  GSM30557: 
+    condition: 35mg/ml benomyl/-benomyl
+  GSM30558: 
+    condition: 40mg/ml benomyl/-benomyl
+  GSM30549: 
+    condition: -benomyl/-benomyl
+  GSM30550: 
+    condition: 1mg/ml benomyl/-benomyl
+  GSM30551: 
+    condition: 5mg/ml benomyl/-benomyl
+:platform: GPL1444

data/install_scripts/GEO/series/GSE1753.yaml

@@ -0,0 +1,16 @@
+--- 
+:title: Pool controls
+:description: |-
+  Determination of how two critical procedural steps in the dSLAM protocol ('diploid synthetic lethality assessed by microarray') affect results
+  Keywords = yeast
+  Keywords = deletion
+  Keywords = synthetic lethality
+  Keywords = tag
+  Keywords = barcode
+  Keywords: ordered
+:arrays: 
+  GSM30547: 
+    condition: sporulation
+  GSM30548: 
+    condition: trnasformation
+:platform: GPL1446

data/install_scripts/GEO/series/GSE1754.yaml

@@ -0,0 +1,19 @@
+--- 
+:title: CIN8 Synthetic Lethality
+:description: |-
+  Assessment of synthetic lethality between a cin8 deletion mutation and Yeast Deletion mutations.
+  Keywords = CIN8
+  Keywords = yeast
+  Keywords = deletion
+  Keywords = synthetic lethality
+  Keywords = tag
+  Keywords = barcode
+  Keywords: repeat sample
+:arrays: 
+  GSM30559: 
+    condition: cin8D dSLAM
+  GSM30560: 
+    condition: cin8D dSLAM
+  GSM30561: 
+    condition: cin8D dSLAM
+:platform: GPL1444

data/install_scripts/GEO/series/GSE1758.yaml

@@ -0,0 +1,15 @@
+--- 
+:title: CDC102 synthetic lethality
+:description: |-
+  Assessment of synthetic lethality between a temperature-sensitive allele of CDC102 and Yeast Deletion mutations
+  Keywords: repeat sample
+:arrays: 
+  GSM30574: 
+    condition: CDC102 wild-type 28C
+  GSM30575: 
+    condition: CDC102 wild-type 30C
+  GSM30572: 
+    condition: cdc102-1 28C
+  GSM30573: 
+    condition: cdc102-1 30C
+:platform: GPL1444

data/install_scripts/GEO/series/GSE1759.yaml

@@ -0,0 +1,18 @@
+--- 
+:title: LCD1-overexpression synthetic lethality
+:description: |-
+  Assessment of synthetic lethality between an overexpressed LCD1 gene and Yeast Deletion mutations
+  Keywords = LCD1
+  Keywords = overexpression
+  Keywords = yeast
+  Keywords = deletion
+  Keywords = synthetic lethality
+  Keywords = tag
+  Keywords = barcode
+  Keywords: repeat sample
+:arrays: 
+  GSM30576: 
+    condition: LCD1over dSLAM
+  GSM30577: 
+    condition: LCD1over dSLAM
+:platform: GPL1444

data/install_scripts/GEO/series/GSE1760.yaml

@@ -0,0 +1,18 @@
+--- 
+:title: TUB1 synthetic haploinsufficiency
+:description: |-
+  Assessment of growth impairment resulting from a heterozygous tub1 null mutation as compared to that from a heterozygous ura3 null mutation
+  Keywords = TUB1
+  Keywords = URA3
+  Keywords = yeast
+  Keywords = deletion
+  Keywords = synthetic haploinsufficiency
+  Keywords = tag
+  Keywords = barcode
+  Keywords: repeat sample
+:arrays: 
+  GSM30578: 
+    condition: tub1D_SHI
+  GSM30579: 
+    condition: tub1D_SHI
+:platform: GPL1444

data/install_scripts/GEO/series/GSE1763.yaml

@@ -0,0 +1,19 @@
+--- 
+:title: Transcriptional effect of aft1 and aft2 mutation in iron depleted conditions
+:description: |-
+  The paralogous transcription factors Aft1p and Aft2p activate the expression of genes involved in iron metabolism under iron depleted conditions. Both are able to bind to the same DNA consensus sequence in vitro. We used DNA microarrays and loss of function mutant strains to better understand the respective roles of Aft1p and Aft2p in the regulation of gene expression
+  Keywords: other
+:arrays: 
+  GSM30663: 
+    condition: wt vs aft1
+  GSM30664: 
+    condition: wt vs aft1
+  GSM30665: 
+    condition: wt vs aft1aft2
+  GSM30666: 
+    condition: wt vs aft1aft2
+  GSM30667: 
+    condition: aft1 vs aft1aft2
+  GSM30668: 
+    condition: aft1 vs aft1aft2
+:platform: GPL205

data/install_scripts/GEO/series/GSE1915.yaml

@@ -0,0 +1,39 @@
+--- 
+:arrays: 
+  GSM34358: 
+    time: HU2h
+  GSM34347: 
+    time: HU4h
+  GSM34348: 
+    time: HU6h
+  GSM34349: 
+    time: HU4h
+  GSM34350: 
+    time: HU2h
+  GSM34351: 
+    time: HU4h
+  GSM34352: 
+    time: HU6h
+  GSM34353: 
+    time: HU1h
+  GSM34354: 
+    time: HU6h
+  GSM34343: 
+    time: HU6h
+  GSM34355: 
+    time: HU2h
+  GSM34344: 
+    time: HU1h
+  GSM34356: 
+    time: HU1h
+  GSM34345: 
+    time: HU2h
+  GSM34357: 
+    time: HU4h
+  GSM34346: 
+    time: HU1h
+:title: CEA_SGF:E00014#HU_response_long-term
+:description: |-
+  Analysis of long-term response to hydroxyurea in a yeast wild-type strain (CDY59). Cells were grown in YPD rich medium containong 200 mM hydroxyurea (HU) during the indicated time (1, 2, 4 or 6 hours). Gene expression changes were analysed compared to the same strain grown in the same medium without HU.
+  Keywords: time-course
+:platform: GPL1531

data/install_scripts/GEO/series/GSE1927.yaml

@@ -0,0 +1,14 @@
+--- 
+:arrays: 
+  GSM34633: 
+    condition: tomatidine_15 uM
+  GSM34634: 
+    condition: tomatidine_7.5 uM
+  GSM34635: 
+    condition: control
+:title: Response of yeast to tomatidine treatment
+:description: "Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the fungistatic saponin tomatidine.\n\
+  Overnight  batch cultures of strain S288C were diluted to an optical density at 600nm of 0.1.  After 1 hour of growth at 30\xC2\xB0C, the compounds were added and the cultures were incubated for an additional 5 hours prior to harvesting. Control cultures were treated with the solvent dimethylformamide (DMF). Tomatidine treated cultures were grown in the presence of tomatidine (dissolved in DMF) at concentations of 7.5 uM and 15 uM.\n\
+  Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen.  Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA).  Microarray hybridisation was performed using the Affymetrix GeneChip\xC2\xAE Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001).   Data were analyzed using Affymetrix\xC2\xAE Microarray Suite version 5.0 software\n\
+  Keywords: dose response"
+:platform: GPL90

data/install_scripts/GEO/series/GSE1941.yaml

@@ -0,0 +1,23 @@
+--- 
+:arrays: 
+  GSM34336: 
+    treatment: BY4742-yap1d 2h
+  GSM34337: 
+    treatment: BY4741-yap1 2h
+  GSM34338: 
+    treatment: BY4741-yap1 2h
+  GSM34339: 
+    treatment: BY4741-yap1 2h
+  GSM34340: 
+    treatment: BY4742-yap1d 2h
+  GSM34341: 
+    treatment: BY4742-yap1d 2h
+  GSM34342: 
+    treatment: BY4741-yap1 2hd
+  GSM34335: 
+    treatment: BY4742-yap1d 2h
+:title: CEA_SGF:E00013#yap1_HU_response
+:description: |-
+  Analysis of the response to hydroxyurea in a yeast yap1 mutant strain compared to wild-type strain (BY4741 or BY4742 backgrounds). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours.
+  Keywords: repeat sample
+:platform: GPL1531

data/install_scripts/GEO/series/GSE1942.yaml

@@ -0,0 +1,31 @@
+--- 
+:arrays: 
+  GSM34369: 
+    condition: aft1d 2h
+  GSM34370: 
+    condition: aft1d aft2d 2h
+  GSM34359: 
+    condition: aft1d aft2d 2h
+  GSM34360: 
+    condition: aft1d 2h
+  GSM34361: 
+    condition: aft1d aft2d 2h
+  GSM34362: 
+    condition: aft1d aft2d 2h
+  GSM34363: 
+    condition: aft1d aft2d 2h
+  GSM34364: 
+    condition: aft1d 2h
+  GSM34365: 
+    condition: aft1d aft2d 2h
+  GSM34366: 
+    condition: aft1d aft2d 2h
+  GSM34367: 
+    condition: aft1d aft2d 2h
+  GSM34368: 
+    condition: aft1d 2h
+:title: CEA_SGF:E00015#aft_HU_response
+:description: |-
+  Analysis of the response to hydroxyurea in a yeast aft1aft2 mutant strain (Y18aft2d) compared to wild-type strain (CM3260). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes due to the aft1 mutation were also analysed in absence of HU (BY4741 background).
+  Keywords: repeat sample
+:platform: GPL1531

data/install_scripts/GEO/series/GSE1944.yaml

@@ -0,0 +1,58 @@
+--- 
+:arrays: 
+  GSM34787: 
+    treatment: Ifh1
+  GSM34776: 
+    treatment: Fhl1
+  GSM34777: 
+    treatment: Fhl1
+  GSM34778: 
+    treatment: Fhl1
+  GSM34779: 
+    treatment: Fhl1
+  GSM34780: 
+    treatment: Ifh1-
+  GSM34781: 
+    treatment: Ifh1-
+  GSM34782: 
+    treatment: Ifh1-
+  GSM34783: 
+    treatment: Ifh1-
+  GSM34772: 
+    treatment: Fhl1-
+  GSM34784: 
+    treatment: Ifh1
+  GSM34773: 
+    treatment: Fhl1-
+  GSM34774: 
+    treatment: Fhl1-
+  GSM34786: 
+    treatment: Ifh1
+  GSM34775: 
+    treatment: Fhl1
+:title: Genome-wide binding of Fhl1 and Ifh1 +/- Rapamycin
+:description: "Array design\n\
+  -Platform: amino-silane coated glass slides (GAPS II, Corning)\n\
+  -S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo \xCE\xB4, etc. A complete description of the primers can be obtained on the web site (ftp://ftp.resgen.com/pub/genepairs/yeast_intergenic).\n\
+  -The PCR products were purified and spotted using an automated arrayer (MicroGrid II, BioRobotics)\n\n\
+  Experiment design\n\
+  -Type of experiment: genome wide binding analysis\n\
+  -Experimental factor: genotype (Wild-Type, Fhl1-myc, Ifh1-myc); drug (rapamycin)\n\
+  -Number of hybridization performed in the experiment: 15 (four conditions with three to five biological replicates each)\n\
+  -Reference used for each condition: ChIP from the wild-type strain\n\
+  -Quality control: one dye-swap per condition\n\
+  Samples used, extract preparation and labeling\n\
+  -The origin of the biological sample:\n\
+  o\tSpecies: S. cerevisiae\n\
+  o\tCell type: (1) W303; (2) W303+IFH1-13myc-TRP1MX6;(3) W303+FHL1-13myc-HIS3MX6.\n\
+  -Growth conditions: log phase (2x107/mL) at 30\xC2\xBAC in YPD medium; when indicated rapamycin was added at the final concentration of 200 ng/mL for 90 min.\n\
+  -Cross-linking for 30 min at 30\xC2\xBAC\n\
+  -Chromatin immunoprecipitation: Dynabeads M280 coupled to sheep anti-mouse IgG or sheep anti-rabbit IgG and mouse monoclonal antibodies against the myc epitope (culture supernatant of 9E10) were used for immunoprecipitation according to standard techniques.\n\
+  -Labeling protocol(s): each IP was blunt-ended, ligated to linker DNA, then subjected to Ligation Mediated (LM)-PCR in the presence of amino-allyl dUTP. Labeling was performed for 1 hour at room temperature in the presence of NHS-ester Cy3 or Cy5 in 0.1 M Sodium Carbonate. The labeling reaction was stopped with 2 M Hydroxylamine and the labeled DNA purified.\n\
+  Hybridization procedures and parameters\n\
+  -Standard protocols were used\n\
+  Measurement data and specifications\n\
+  -Software for scanning: GenePix Pro 4.0 (Axon Instruments, Inc.)\n\
+  -Scanner: GenePix 4000A (Axon Instruments, Inc.)\n\
+  Keywords: dose response"
+:platform: GPL1695