rbbt-marq 1.0.0

data/install_scripts/GEO/series/GSE10933.yaml

@@ -0,0 +1,15 @@
+--- 
+:arrays: 
+  GSM277251: 
+    condition: mutH3
+  GSM277242: 
+    condition: wtH3
+  GSM277243: 
+    condition: wtH3
+  GSM277250: 
+    condition: mutH3
+: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 K4,9,14,18,23,27,36,79G mutant.
+  Keywords: repeat
+:title: Histone H3 K4,9,14,18,23,27,36,79G
+:platform: GPL90

data/install_scripts/GEO/series/GSE10944.yaml

@@ -0,0 +1,21 @@
+--- 
+:arrays: 
+  GSM277437: 
+    time: meiosis 8h
+  GSM277431: 
+    time: meiosis 1h
+  GSM277432: 
+    time: meiosis 2h
+  GSM277433: 
+    time: meiosis 3h
+  GSM277434: 
+    time: meiosis 4h
+  GSM277435: 
+    time: meiosis 5h
+  GSM277436: 
+    time: meiosis 6h
+:description: |-
+  We studied the meiotic regulation of transcription, by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h.
+  Keywords: yeast meiotic time course, transcriptome
+:title: Transcriptomic regulation during meiosis
+:platform: GPL6649

data/install_scripts/GEO/series/GSE10947.yaml

@@ -0,0 +1,21 @@
+--- 
+:arrays: 
+  GSM277461: 
+    time: meiosis Spo11Y135F mutant 1h
+  GSM277462: 
+    time: meiosis Spo11Y135F mutant 2h
+  GSM277463: 
+    time: meiosis Spo11Y135F mutant 3h
+  GSM277464: 
+    time: meiosis Spo11Y135F mutant 4h
+  GSM277465: 
+    time: meiosis Spo11Y135F mutant 5h
+  GSM277467: 
+    time: meiosis Spo11Y135F mutant 6h
+  GSM277468: 
+    time: meiosis Spo11Y135F mutant 8h
+:description: |-
+  We studied the meiotic regulation of transcription in the mutant Spo11Y135F (deficient for the formation of meiotic double-strand breaks), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h.
+  Keywords: yeast meiotic time course, transcriptome
+:title: Transcriptomic regulation during meiosis (Spo11Y135F mutant)
+:platform: GPL6649

data/install_scripts/GEO/series/GSE10948.yaml

@@ -0,0 +1,21 @@
+--- 
+:arrays: 
+  GSM277471: 
+    condition: Clb5Delta-Clb6Delta mutant meiosis 2h
+  GSM277472: 
+    condition: Clb5Delta-Clb6Delta mutant meiosis 3h
+  GSM277473: 
+    condition: Clb5Delta-Clb6Delta mutant meiosis 4h
+  GSM277474: 
+    condition: Clb5Delta-Clb6Delta mutant meiosis 5h
+  GSM277475: 
+    condition: Clb5Delta-Clb6Delta mutant meiosis 8h
+  GSM277476: 
+    condition: Clb5Delta-Clb6Delta mutant meiosis 6h
+  GSM277470: 
+    condition: Clb5Delta-Clb6Delta mutant meiosis 1h
+:description: |-
+  We studied the meiotic regulation of transcription in the mutant Clb5Delta-Clb6Delta (deficient for the meiotic replication), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h.
+  Keywords: yeast meiotic time course, transcriptome
+:title: Transcriptomic regulation during meiosis (Clb5Delta-Clb6Delta mutant)
+:platform: GPL6649

data/install_scripts/GEO/series/GSE11061.yaml

@@ -0,0 +1,19 @@
+--- 
+:arrays: 
+  GSM279641: 
+    treatment: control
+  GSM279642: 
+    treatment: CSF-1
+  GSM279643: 
+    treatment: control
+  GSM279644: 
+    treatment: CSF-1
+  GSM279640: 
+    treatment: CSF-1
+  GSM279639: 
+    treatment: control
+:description: |-
+  Although the role of macrophage colony stimulating factor (M-CSF/CSF-1) in homeostasis and disease processes has been studied extensively in mice, little is known of the impact of this cytokine on differentiated human macrophages. Here we show that, in contrast to its effects on mouse bone marrow-derived macrophages (BMM), CSF-1 did not induce expression of urokinase plasminogen activator mRNA, repress expression of apolipoprotein E mRNA, or prime LPS-induced TNF secretion in human monocyte-derived macrophages (HMDM) from several independent donors. Using expression profiling, we show that CSF-1 dynamically regulated the expression of several genes that encode chemokines and chemokine receptors (e.g. CXCL10/IP-10, CXCL2, CCL7, SDF2L1, CXCR4) in HMDM. CSF-1 also upregulated the expression of several genes encoding enzymes of the cholesterol biosynthetic pathway (HMGCR, MVD, IDI1, FDPS, SQLE, CYP51A1, EBP, NSDHL, DHCR7 and DHCR24), while expression of ABCG1, encoding a cholesterol efflux transporter, was repressed. Although the CSF-1/CSF-1R system has been proposed as a target for the treatment of inflammatory and metastatic disease based on studies in rodents, this is the first systematic analysis of the effects of CSF-1 on mature human macrophages. Our data demonstrates that CSF-1 represents a further link between inflammation and cardiovascular disease, inflammtion and immunity.
+  Keywords: Stimulus response
+:title: Colony Stimulating Factor 1 (CSF-1) responses in human monocyte derived macrophages
+:platform: GPL2507

data/install_scripts/GEO/series/GSE11071.yaml

@@ -0,0 +1,67 @@
+--- 
+:arrays: 
+  GSM280330: 
+    treatment: C1 evolved M5 vs YFP
+  GSM280319: 
+    treatment: C1 evolved M1 vs GFP
+  GSM280308: 
+    treatment: C1 evolved control YFP vs GFP
+  GSM280320: 
+    treatment: C1 evolved M3 vs YFP
+  GSM280309: 
+    treatment: C1 evolved M5 vs YFP
+  GSM280321: 
+    treatment: C1 evolved control YFP vs DsRED
+  GSM280310: 
+    treatment: C1 evolved control YFP vs GFP
+  GSM280322: 
+    treatment: C1 evolved M2 vs DsRED
+  GSM280311: 
+    treatment: C1 evolved control GFP vs DsRED
+  GSM280323: 
+    treatment: C1 evolved M2 vs DsRED
+  GSM280301: 
+    treatment: C1 evolved M4 vs DsRED
+  GSM280324: 
+    treatment: C1 evolved M4 vs DsRED
+  GSM280313: 
+    treatment: C1 evolved M1 vs GFP
+  GSM280302: 
+    treatment: C1 evolved M1 vs GFP
+  GSM280325: 
+    treatment: C1 evolved M3 vs YFP
+  GSM280314: 
+    treatment: C1 evolved control GFP vs DsRED
+  GSM280303: 
+    treatment: C1 evolved M2 vs DsRED
+  GSM280326: 
+    treatment: C1 evolved M3 vs YFP
+  GSM280315: 
+    treatment: C1 evolved control YFP vs DsRED
+  GSM280304: 
+    treatment: C1 evolved M4 vs DsRED
+  GSM280327: 
+    treatment: C1 evolved M5 vs YFP
+  GSM280316: 
+    treatment: C1 evolved M2 vs DsRED
+  GSM280305: 
+    treatment: C1 evolved M5 vs YFP
+  GSM280328: 
+    treatment: C1 evolved M4 vs DsRED
+  GSM280317: 
+    treatment: C1 evolved control DsRED vs GFP
+  GSM280306: 
+    treatment: C1 evolved M5 vs YFP
+  GSM280329: 
+    treatment: C1 evolved M4 vs DsRED
+  GSM280318: 
+    treatment: C1 evolved M1 vs GFP
+  GSM280307: 
+    treatment: C1 evolved control YFP vs GFP
+:description: |-
+  Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents.
+  An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
+  Genotype: Evolved clones.  The genotype is not necessarily complete.
+  Keywords: all_pairs
+:title: C1 evolved adaptive clones M1-M5
+:platform: GPL6720

data/install_scripts/GEO/series/GSE11111.yaml

@@ -0,0 +1,25 @@
+--- 
+:arrays: 
+  GSM280154: 
+    treatment: BY11g BY4716 0 2 glucose
+  GSM280155: 
+    treatment: BY7g BY4716 0 2 glucose
+  GSM280156: 
+    treatment: BY9g BY4716 0 2 glucose
+  GSM280157: 
+    treatment: RM11g RM11-1a 0 2 glucose
+  GSM280158: 
+    treatment: RM7g RM11-1a 0 2 glucose
+  GSM280159: 
+    treatment: RM9g RM11-1a 0 2 glucose
+  GSM280160: 
+    treatment: YAD350 (YLK723) glucose vs mixed reference
+  GSM280161: 
+    treatment: YLK804 glucose vs mixed reference
+  GSM280162: 
+    treatment: YLK806 glucose vs mixed reference
+:description: |-
+  A major goal of biology is the construction of networks that predict complex system behavior.  We combine multiple types of molecular data, including genotypic, expression, transcription factor binding site (TFBS), and protein-protein interaction (PPI) data previously generated from a number of yeast experiments in order to reconstruct causal gene networks.  Networks based on different types of data are compared using metrics devised to assess the predictive power of a network.  A network reconstructed by integrating genotypic, TFBS and PPI data is shown to be the most predictive. This network is used to predict causal regulators responsible for hot spots of gene expression activity in a segregating yeast population.  The network is also shown to elucidate the mechanisms by which causal regulators give rise to larger-scale changes in gene expression activity.  Predictions are prospectively validated to provide direct experimental evidence that predictive networks can be constructed by integrating multiple, appropriate data types.
+  Keywords: allele replacement
+:title: Integrating Large-Scale Functional Genomic Data to Dissect the Complexity of Yeast Regulatory Networks
+:platform: GPL2883

data/install_scripts/GEO/series/GSE11236.yaml

@@ -0,0 +1,25 @@
+--- 
+:arrays: 
+  GSM283150: 
+    condition: cth1cth2 in 100uM BPS
+  GSM283151: 
+    condition: cth1cth2 in 100uM BPS
+  GSM283152: 
+    condition: cth1cth2 in 100uM BPS
+  GSM283153: 
+    condition: CTH1cth2 in 100uM BPS
+  GSM283154: 
+    condition: CTH1cth2 in 100uM BPS
+  GSM283155: 
+    condition: CTH1cth2 in 100uM BPS
+  GSM283156: 
+    condition: cth1CTH2 in 100uM BPS
+  GSM283157: 
+    condition: cth1CTH2 in 100uM BPS
+  GSM283158: 
+    condition: cth1CTH2 in 100uM BPS
+:description: |-
+  Expression of the yeast Cth2 protein stimulates degradation of mRNAs encoding proteins with Fe-dependent functions in metabolism, in iron storage and in other cellular processes. We demonstrate that in response to Fe deprivation, the Cth2-homologue, Cth1, stimulates specific degradation of mRNAs involved in mitochondrially localized activities that include respiration and amino acid biosynthesis. Furthermore, yeast cells grown under Fe deprivation accumulate mRNAs encoding proteins that function in glucose metabolism.  These studies demonstrate a reprogramming of cellular metabolism during Fe-starvation dependent on the coordinated activities of two mRNA binding proteins.
+  Keywords: Messenger RNAs down regulated by Cth1 and Cth2 proteins in response to Fe-limitation
+:title: Cooperation of two mRNA-binding proteins drives metabolic adaptation to iron deficiency
+:platform: GPL90

data/install_scripts/GEO/series/GSE11282.yaml

@@ -0,0 +1,19 @@
+--- 
+:arrays: 
+  GSM284868: 
+    condition: Wild type for H4 R45H
+  GSM284869: 
+    condition: Wild type for H4 R45H
+  GSM284870: 
+    condition: Wild type for H4 R45H
+  GSM284871: 
+    condition: Mutant histone H4R45H
+  GSM284872: 
+    condition: Mutant histone H4R45H
+  GSM284873: 
+    condition: Mutant histone H4R45H
+:description: |-
+  Total RNA samples from three replicate cultures of wild type and mutant yeast strains was isolated and expression profile done using Affymetrix arrays. Comparsion between the samples indicate how mutation in a single amino acid residue in histone H4 (H4R45H) affects gene expression in yeast. Such a mutation in histone H4 is known to generate a specific class of mutants called SWI/SNF independent (SIN) mutants, and the mutants were identified by their ability to carry out transcription in the absence of yeast chromatin remodeling complex SWI/SNF. SIN mutations are known to affect higher order chromatin structure and the comparative expression profile would help identification  of genes which get affected by such altered chromatin landscape.
+  Keywords: mutant analysis
+:title: Comparison of yeast (Saccharomyces cerevisiae) strain with histone H4 R45 mutated to H with wild type yeast strain WY139
+:platform: GPL2529

data/install_scripts/GEO/series/GSE11377.yaml

@@ -0,0 +1,19 @@
+--- 
+:arrays: 
+  GSM287287: 
+    condition: ada2wt vs. ada2rlr
+  GSM287276: 
+    condition: ada2wt vs. ada2rlr
+  GSM287248: 
+    condition: ADA2 vs. ada2delta
+  GSM287215: 
+    condition: ADA2 vs. ada2delta
+  GSM287249: 
+    condition: ADA2 vs. ada2delta
+  GSM287251: 
+    condition: ada2wt vs. ada2rlr
+:description: |-
+  The SAGA complex of Saccharomyces cerevisiae contains greater than 20 components that acetylate and deubiquitylate nucleosomal histones. Its acetyltransferase, Gcn5 preferentially acetylates histones H3 and H2B and is regulated through interactions with Ada2 and Ngg1/Ada3. The N-terminal region of Ada2 contains a SANT domain that contacts Gcn5 near its catalytic site. Sequence alignments of Ada2 homologues indicate a conserved ~120 amino acid residue central region that interacts with Ngg1.To examine the function of this central region, we constructed ada2 alleles with mutations of clustered conserved residues. One of these alleles, ada2-RLR, resulted in a ~3-fold reduction in transcriptional activation of the PHO5 gene and growth changes that parallel deletion of ada2. Microarray analyses further revealed that ada2-RLR  alters expression of a subset of those genes affected by deletion of ada2.
+  Keywords: yeast, Ada2, SAGA complex, gene expression, genetic modification
+:title: The role of the central region of Ada2 in gene regulation
+:platform: GPL884

data/install_scripts/GEO/series/GSE11380.yaml

@@ -0,0 +1,13 @@
+--- 
+:arrays: 
+  GSM287511: 
+    mutant: wild type vs ace2
+  GSM287512: 
+    mutant: wild type vs swi5
+  GSM287513: 
+    mutant: wild type vs ace2swi5
+:description: |-
+  The homologous Ace2 and Swi5 transcription factors of Saccharomyces cerevisiae have identical DNA-binding domains, and both are cell cycle regulated. There are common target genes, as well as genes activated only by Ace2 and other genes activated only by Swi5.
+  Keywords: genetic modification
+:title: Regulation by the homologous Ace2 and Swi5 factors of Saccharomyces cerevisiae
+:platform: GPL2883

data/install_scripts/GEO/series/GSE11397.yaml

@@ -0,0 +1,55 @@
+--- 
+:arrays: 
+  GSM287748: 
+    treatment: med20 vs wt diax
+  GSM287737: 
+    treatment: med20  /- rap
+  GSM287749: 
+    treatment: med20 vs wt diax
+  GSM287738: 
+    treatment: med20 vs wt rap
+  GSM287750: 
+    treatment: med16 vs wt rap
+  GSM287739: 
+    treatment: med20 vs wt rap
+  GSM287751: 
+    treatment: med16 vs wt rap
+  GSM287740: 
+    treatment: med20 vs wt chlo
+  GSM287752: 
+    treatment: med31 vs wt rap
+  GSM287741: 
+    treatment: med20 vs wt chlo
+  GSM287753: 
+    treatment: med31 vs wt rap
+  GSM287742: 
+    treatment: med20 vs wt tun
+  GSM287754: 
+    treatment: cycC vs wt rap
+  GSM287743: 
+    treatment: med20 vs wt tun
+  GSM287732: 
+    treatment: med20 vs wt
+  GSM287755: 
+    treatment: cycC vs wt rap
+  GSM287744: 
+    treatment: med20 vs wt H2O2
+  GSM287733: 
+    treatment: med20 vs wt
+  GSM287745: 
+    treatment: med20 vs wt H2O2
+  GSM287734: 
+    treatment: wt /- rap
+  GSM287746: 
+    treatment: med20 vs wt heat
+  GSM287735: 
+    treatment: wt /- rap
+  GSM287747: 
+    treatment: med20 vs wt heat
+  GSM287736: 
+    treatment: med20  /- rap
+:description: |-
+  Transcriptional repression of ribosomal components and tRNAs is coordinately regulated in response to a wide variety of environmental stresses. Part of this response involves the convergence of different nutritional and stress signaling pathways on Maf1, a protein that is essential for repressing transcription by RNA polymerase (pol) III in Saccharomyces cerevisiae. Here we identify the functions buffering yeast cells that are unable to down-regulate transcription by RNA pol III. MAF1 genetic interactions identified in screens of non-essential gene-deletions and conditionally-expressed essential genes reveal a highly interconnected network of 64 genes involved in ribosome biogenesis, RNA pol II transcription, tRNA modification, ubiquitin-dependent proteolysis and other processes. A survey of non-essential MAF1 synthetic sick/lethal (SSL) genes identified six gene-deletions that are defective in transcriptional repression of ribosomal protein (RP) genes following rapamycin treatment. This subset of MAF1 SSL genes included MED20 which encodes a head module subunit of the RNA pol II Mediator complex. Genetic interactions between MAF1 and subunits in each structural module of Mediator were investigated to examine the functional relationship between these transcriptional regulators. Gene expression profiling identified a prominent and highly selective role for Med20 in the repression of RP gene transcription following treatments with rapamycin, chlorpromazine and tunicamycin and in post-diauxic cells. In addition, attenuated repression of RP genes by rapamycin was observed in a strain deleted for the Mediator tail module subunit Med16. The data suggest that Mediator and Maf1 function in parallel pathways to negatively regulate RP mRNA and tRNA synthesis.
+  Keywords: genetic modification, stress response
+:title: Effects of Mediator subunit gene-deletions under conditions that repress ribosome synthesis
+:platform: GPL1229

data/install_scripts/GEO/series/GSE11412.yaml

@@ -0,0 +1,11 @@
+--- 
+:arrays: 
+  GSM287991: 
+    treatment: wt
+  GSM287992: 
+    treatment: alpha-factor
+:description: |-
+  We measured the response of S. cerevisiae to arrest in the presence of alpha factor.  These were collected in support of a related DNaseI-sequencing study.
+  Keywords: Alpha-factor arrest
+:title: Alpha-factor treatment of Saccharomyces cerevisiae
+:platform: GPL2529

data/install_scripts/GEO/series/GSE11452.yaml

@@ -0,0 +1,354 @@
+--- 
+:arrays: 
+  GSM291448: 
+    condition: Iron limited chemostat cultures with ethanol as a carbon source
+  GSM290691: 
+    condition: Acetate limited chemostat culture D=0.1/h
+  GSM200686: 
+    condition: Carbon-limited Aerobic chemostat culture
+  GSM29946: 
+    condition: Anaerobic phosphorus limited
+  GSM296157: 
+    condition: Anaerobic nitrogen limited chemostat 0.03h-1
+  GSM291449: 
+    condition: Iron limited chemostat cultures with ethanol as a carbon source
+  GSM290692: 
+    condition: Ethanol limited chemostat culture D=0.1/h
+  GSM200687: 
+    condition: Carbon-limited Aerobic chemostat culture
+  GSM296158: 
+    condition: Anaerobic glucose limited chemostat
+  GSM200688: 
+    condition: Nitrogen-limited Aerobic chemostat culture
+  GSM29948: 
+    condition: Anaerobic sulfur limited
+  GSM296159: 
+    condition: Aerobic glucose limited chemostat with 25 mM formate
+  GSM291420: 
+    condition: Aerobic glucose limited chemostat with Phenylalanine as N-source
+  GSM200689: 
+    condition: Nitrogen-limited Aerobic chemostat culture
+  GSM29949: 
+    condition: Anaerobic sulfur limited
+  GSM317647: 
+    condition: C-lim aerobic chemostat with 25mM formate
+  GSM283692: 
+    condition: C-lim Anaerobic chemostat dilution rate 0.05h-1
+  GSM29920: 
+    condition: Aerobic nitrogen limited
+  GSM283693: 
+    condition: C-lim Anaerobic chemostat dilution rate 0.05h-1
+  GSM200690: 
+    condition: Nitrogen-limited Aerobic chemostat culture
+  GSM283694: 
+    condition: C-lim Anaerobic chemostat dilution rate 0.05h-1
+  GSM200691: 
+    condition: Nitrogen-limited Anaerobic chemostat culture
+  GSM137497: 
+    condition: C-lim Anaerobic reference (pH 5)
+  GSM283695: 
+    condition: erobic galactose C-lim chemostat culture
+  GSM29922: 
+    condition: Aerobic nitrogen limited
+  GSM137498: 
+    condition: C-lim Anaerobic reference (pH 5)
+  GSM29951: 
+    condition: Anaerobic sulfur limited
+  GSM283696: 
+    condition: erobic galactose C-lim chemostat culture
+  GSM200692: 
+    condition: Nitrogen-limited Anaerobic chemostat culture
+  GSM291340: 
+    condition: Aerobic phosphorus limited chemostat with anaerobic factors (tween and ergosterol)
+  GSM283697: 
+    condition: erobic galactose C-lim chemostat culture
+  GSM29924: 
+    condition: Aerobic phosphorus limited
+  GSM200693: 
+    condition: Nitrogen-limited Anaerobic chemostat culture
+  GSM291341: 
+    condition: Aerobic phosphorus limited chemostat with anaerobic factors (tween and ergosterol)
+  GSM283698: 
+    condition: erobic galactose C-lim chemostat culture
+  GSM291342: 
+    condition: Aerobic phosphorus limited chemostat with anaerobic factors (tween and ergosterol)
+  GSM283868: 
+    condition: Aerobic S-lim chemostat culture
+  GSM283699: 
+    condition: erobic galactose C-lim chemostat culture
+  GSM29926: 
+    condition: Aerobic phosphorus limited
+  GSM198364: 
+    condition: Zinc limited Aerobic chemostat culture
+  GSM108392: 
+    condition: Aerobic glucose limited
+  GSM291343: 
+    condition: Anaerobic glucose limited chemostat with methionine as sulfur source
+  GSM284058: 
+    condition: N-lim Anaerobic chemostat dilution rate 0.2h-1
+  GSM283897: 
+    condition: Aerobic pH3.5 C-lim chemostat culture
+  GSM283869: 
+    condition: Aerobic S-lim chemostat culture
+  GSM147746: 
+    condition: C-lim aerobic chemostat with ASN as N-source
+  GSM29927: 
+    condition: Aerobic phosphorus limited
+  GSM198365: 
+    condition: Zinc limited Aerobic chemostat culture
+  GSM108393: 
+    condition: Aerobic glucose limited
+  GSM291344: 
+    condition: Anaerobic glucose limited chemostat with methionine as sulfur source
+  GSM284059: 
+    condition: N-lim Anaerobic chemostat dilution rate 0.2h-1
+  GSM283898: 
+    condition: Aerobic pH3.5 C-lim chemostat culture
+  GSM147747: 
+    condition: C-lim aerobic chemostat with ASN as N-source
+  GSM198366: 
+    condition: Zinc limited Aerobic chemostat culture
+  GSM108394: 
+    condition: Aerobic glucose limited
+  GSM291345: 
+    condition: Anaerobic glucose limited chemostat with methionine as sulfur source
+  GSM283899: 
+    condition: Aerobic pH3.5 C-lim chemostat culture
+  GSM147748: 
+    condition: C-lim aerobic chemostat with ASN as N-source
+  GSM29929: 
+    condition: Aerobic sulfur limited
+  GSM198367: 
+    condition: Zinc-limited Anaerobic chemostat culture
+  GSM143071: 
+    condition: 12C Chemostat anaerobic C-lim 0.03h-1
+  GSM291346: 
+    condition: Anaerobic nitrogen limited chemostat with methionine as nitrogen source
+  GSM108368: 
+    condition: Anaerobic carbon limited
+  GSM147749: 
+    condition: C-lim aerobic chemostat with Proline as N-source
+  GSM198368: 
+    condition: Zinc-limited Anaerobic chemostat culture
+  GSM234643: 
+    condition: Carbon-limited anaerobic chemostat with benzoate
+  GSM291347: 
+    condition: Anaerobic nitrogen limited chemostat with methionine as nitrogen source
+  GSM284060: 
+    condition: C-lim Anaerobic chemostat dilution rate 0.03h-1
+  GSM283870: 
+    condition: C-lim Anaerobic chemostat dilution rate 0.03h-1
+  GSM283700: 
+    condition: erobic galactose C-lim chemostat culture
+  GSM108369: 
+    condition: Anaerobic carbon limited
+  GSM198369: 
+    condition: Zinc-limited Anaerobic chemostat culture
+  GSM234644: 
+    condition: Carbon-limited anaerobic chemostat with benzoate
+  GSM143073: 
+    condition: 12C Chemostat anaerobic C-lim 0.03h-1
+  GSM291431: 
+    condition: Aerobic glucose limited chemostat with Phenylalanine as N-source
+  GSM291348: 
+    condition: Anaerobic nitrogen limited chemostat with methionine as nitrogen source
+  GSM284061: 
+    condition: C-lim Anaerobic chemostat dilution rate 0.03h-1
+  GSM283871: 
+    condition: N-lim Anaerobic chemostat dilution rate 0.03h-1
+  GSM225399: 
+    condition: Ethanol limited chemostat D=0.1/h
+  GSM234645: 
+    condition: Carbon-limited anaerobic chemostat with benzoate
+  GSM225482: 
+    condition: Anaerobic glucose limited chemostat cultureCO2
+  GSM291432: 
+    condition: Aerobic glucose limited chemostat with leucine as nitrogen source
+  GSM291349: 
+    condition: Anaerobic nitrogen limited chemostat with methionine as nitrogen and sulfur source
+  GSM283872: 
+    condition: C-lim Anaerobic chemostat dilution rate 0.2h-1
+  GSM147750: 
+    condition: C-lim aerobic chemostat with Proline as N-source
+  GSM29930: 
+    condition: Aerobic sulfur limited
+  GSM209979: 
+    condition: CENPK113-7D glucose/ethanol limited chemostat
+  GSM283900: 
+    condition: Aerobic pH6.5 C-lim chemostat culture
+  GSM283873: 
+    condition: C-lim Anaerobic chemostat dilution rate 0.2h-1
+  GSM283901: 
+    condition: Aerobic pH6.5 C-lim chemostat culture
+  GSM108370: 
+    condition: Anaerobic carbon limited
+  GSM147751: 
+    condition: C-lim aerobic chemostat with Proline as N-source
+  GSM137675: 
+    condition: C-lim Anaerobic reference (pH 5)
+  GSM29932: 
+    condition: Aerobic sulfur limited
+  GSM143076: 
+    condition: 12C Chemostat anaerobic C-lim 0.03h-1
+  GSM137676: 
+    condition: C-lim Anaerobic Acetate
+  GSM143077: 
+    condition: 30C Anaerobic C-lim chemostat 0.03h-1
+  GSM209980: 
+    condition: CENPK113-7D glucose/ethanol limited chemostat
+  GSM291350: 
+    condition: Anaerobic nitrogen limited chemostat with methionine as nitrogen and sulfur source
+  GSM283903: 
+    condition: Aerobic pH6.5 C-lim chemostat culture
+  GSM137677: 
+    condition: C-lim Anaerobic Acetate
+  GSM29934: 
+    condition: Anaerobic carbon limited
+  GSM209981: 
+    condition: CENPK113-7D glucose/ethanol limited chemostat
+  GSM147753: 
+    condition: C-lim aerobic chemostat with leucine as N-source
+  GSM291351: 
+    condition: Anaerobic nitrogen limited chemostat with methionine as nitrogen and sulfur source
+  GSM225514: 
+    condition: Anaerobic glucose limited chemostat cultureCO2
+  GSM137678: 
+    condition: C-lim Anaerobic Acetate
+  GSM143079: 
+    condition: 30C Anaerobic C-lim chemostat 0.03h-1
+  GSM209982: 
+    condition: CENPK113-7D glucose/ethanol limited chemostat
+  GSM225400: 
+    condition: Ethanol limited chemostat D=0.1/h
+  GSM147754: 
+    condition: C-lim aerobic chemostat with leucine as N-source
+  GSM225515: 
+    condition: Aerobic glucose limited chemostat cultureCO2
+  GSM137679: 
+    condition: C-lim Anaerobic Benzoate
+  GSM225401: 
+    condition: Ethanol limited chemostat D=0.1/h
+  GSM147755: 
+    condition: C-lim aerobic chemostat with leucine as N-source
+  GSM225402: 
+    condition: Acetate limited chemostat culture D=0.1/h
+  GSM225516: 
+    condition: Aerobic glucose limited chemostat cultureCO2
+  GSM225403: 
+    condition: Acetate limited chemostat culture D=0.1/h
+  GSM147757: 
+    condition: C-lim aerobic chemostat with phenylalanine as N-source
+  GSM225517: 
+    condition: Aerobic glucose limited chemostat cultureCO2
+  GSM29939: 
+    condition: Anaerobic nitrogen limited
+  GSM137680: 
+    condition: C-lim Anaerobic Benzoate
+  GSM143081: 
+    condition: 30C Anaerobic C-lim chemostat 0.03h-1
+  GSM225404: 
+    condition: Acetate limited chemostat culture D=0.1/h
+  GSM147758: 
+    condition: C-lim aerobic chemostat with phenylalanine as N-source
+  GSM291100: 
+    condition: Anaerobic carbon limited with methionine as N-source
+  GSM137681: 
+    condition: C-lim Anaerobic Benzoate
+  GSM143082: 
+    condition: 12C anaerobic N-lim chemostat 0.03h-1
+  GSM147759: 
+    condition: C-lim aerobic chemostat with methionine as N-source
+  GSM225519: 
+    condition: Aerobic nitrogen limited chemostat cultureCO2
+  GSM137682: 
+    condition: C-lim Anaerobic Propionate
+  GSM143083: 
+    condition: 12C anaerobic N-lim chemostat 0.03h-1
+  GSM317639: 
+    condition: Aerobic sulfur limited culture (cDNA from total RNA)
+  GSM137683: 
+    condition: C-lim Anaerobic Propionate
+  GSM143084: 
+    condition: 12C anaerobic N-lim chemostat 0.03h-1
+  GSM225407: 
+    condition: Maltose limited chemostat culture D=0.1/h
+  GSM317837: 
+    condition: CENPK113-7D glucose/ethanol (19mM) limited chemostat
+  GSM291103: 
+    condition: Anaerobic carbon limited with methionine as N-source
+  GSM29940: 
+    condition: Anaerobic nitrogen limited
+  GSM143085: 
+    condition: 30C anaerobic N-lim chemostat 0.03h-1
+  GSM29912: 
+    condition: Aerobic glucose limited
+  GSM225520: 
+    condition: Aerobic nitrogen limited chemostat cultureCO2
+  GSM137684: 
+    condition: C-lim Anaerobic Propionate
+  GSM317838: 
+    condition: CENPK113-7D glucose/ethanol (19mM) limited chemostat
+  GSM291104: 
+    condition: Anaerobic carbon limited with methionine as N-source
+  GSM290744: 
+    condition: N-lim Anaerobic chemostat dilution rate 0.2h-1
+  GSM147761: 
+    condition: C-lim aerobic chemostat with methionine as N-source
+  GSM137685: 
+    condition: C-lim Anaerbic Sorbate
+  GSM317839: 
+    condition: CENPK113-7D glucose/ethanol (19mM) limited chemostat
+  GSM291105: 
+    condition: Aerobic glucose limited chemostat with anaerobic factors (tween and ergosterol)
+  GSM290745: 
+    condition: N-lim Anaerobic chemostat dilution rate 0.03h-1
+  GSM29914: 
+    condition: Aerobic glucose limited
+  GSM225521: 
+    condition: Aerobic nitrogen limited chemostat cultureCO2
+  GSM29942: 
+    condition: Anaerobic nitrogen limited
+  GSM291106: 
+    condition: Aerobic glucose limited chemostat with anaerobic factors (tween and ergosterol)
+  GSM290746: 
+    condition: N-lim Anaerobic chemostat dilution rate 0.2h-1
+  GSM147762: 
+    condition: C-lim aerobic chemostat with methionine as N-source
+  GSM137686: 
+    condition: C-lim Anaerbic Sorbate
+  GSM29943: 
+    condition: Anaerobic phosphorus limited
+  GSM291418: 
+    condition: Anaerobic sulfur limited chemostat
+  GSM291107: 
+    condition: Aerobic glucose limited chemostat with anaerobic factors (tween and ergosterol)
+  GSM137687: 
+    condition: C-lim Anaerbic Sorbate
+  GSM143088: 
+    condition: 30C anaerobic N-lim chemostat 0.03h-1
+  GSM317840: 
+    condition: C-lim Aerobic chemostat with maltose as C-source
+  GSM291419: 
+    condition: Aerobic glucose limited chemostat with Phenylalanine as N-source
+  GSM29917: 
+    condition: Aerobic glucose limited
+  GSM200685: 
+    condition: Carbon-limited Aerobic chemostat culture
+  GSM225469: 
+    condition: Anaerobic glucose limited chemostat cultureCO2
+  GSM29945: 
+    condition: Anaerobic phosphorus limited
+  GSM143089: 
+    condition: 30C anaerobic N-lim chemostat 0.03h-1
+:description: |-
+  Background
+  Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on transcriptional regulation. Steady-state chemostat cultures, which do enable accurate control, measurement and manipulation of individual cultivation parameters (e.g. specific growth rate, temperature, identity of the growth-limiting nutrient) appear to provide a promising experimental platform for such a combinatorial analysis.
+  Results
+  A microarray compendium of 170 steady-state chemostat cultures of the yeast Saccharomyces cerevisiae is presented and analyzed. The 170 microarrays encompass 55 unique conditions, which can be characterized by the combined settings of 10 different cultivation parameters.
+  By applying a regression model to assess the impact of (combinations of) cultivation parameters on the transcriptome, most S. cerevisiae genes were shown to be influenced by multiple cultivation parameters, and in many cases by combinatorial effects of cultivation parameters. The inclusion of these combinatorial effects in the regression model led to higher explained variance of the gene expression patterns and resulted in higher function enrichment in subsequent analysis.
+  We further demonstrate the usefulness of the compendium and regression analysis for interpretation of shake-flask-based transcriptome studies and for guiding functional analysis of (uncharacterized) genes and pathways.
+  Conclusions
+  Modeling the combinatorial effects of environmental parameters on the transcriptome is crucial for understanding transcriptional regulation. Chemostat cultivation offers a powerful tool for such an approach.
+  Keywords: chemostat steady state samples
+:title: Saccharomyces cerevisiae chemostat steady state microarray compendium
+:platform: GPL90