MARQ 0.0.1

data/install_scripts/GEO/series/GSE7369.yaml

@@ -0,0 +1,15 @@
+--- 
+:description: |-
+  We transcriptional profiled four transcription factor knockout strains in S288C background growing in YNB media + 2% glucose to understand the link between mRNA levels and our measured C13 fluxes of amino acid biosynthesis.  We conducted this analysis as a follow up to our work on the Gcn4p transcription factor.
+  Keywords: genetic modification
+:arrays: 
+  GSM177371: 
+    condition: Met28 knockout expression
+  GSM177372: 
+    condition: Met31 knockout expression
+  GSM177373: 
+    condition: Met32 knockout expression
+  GSM177374: 
+    condition: Cbf1 knockout expression
+:title: Transcriptional control of amino acid biosynthesis
+:platform: GPL5043

data/install_scripts/GEO/series/GSE7525.yaml

@@ -0,0 +1,33 @@
+--- 
+:arrays: 
+  GSM182236: 
+    treatment: S.cerevisiae_mating_90min
+  GSM182225: 
+    treatment: S.cerevisiae_alpha_factor_60min
+  GSM182226: 
+    treatment: S.cerevisiae_alpha_factor_60min
+  GSM182227: 
+    treatment: S.paradoxus_alpha_factor_60min
+  GSM182228: 
+    treatment: S.paradoxus_alpha_factor_60min
+  GSM182229: 
+    treatment: S.paradoxus_alpha_factor_60min
+  GSM182230: 
+    treatment: S.mikatae_alpha_factor_60min
+  GSM182231: 
+    treatment: S.mikatae_alpha_factor_60min
+  GSM182232: 
+    treatment: S.mikatae_alpha_factor_60min
+  GSM182233: 
+    treatment: S.mikatae_alpha_factor_60min
+  GSM182234: 
+    treatment: S.cerevisiae_mating_90min
+  GSM182235: 
+    treatment: S.cerevisiae_mating_90min
+  GSM182224: 
+    treatment: S.cerevisiae_alpha_factor_60min
+:description: |-
+  We examined the mating response of three yeast species, by subjecting a-type cells from each of them to alpha-factor (6uM). The expression of cells before and after (60min) addition of alpha-factor were compared using S. cerevisiae cDNA microarrays. In addition, we verified our results with a true mating experiment: the expression of a-type and alpha-type cells from S. cerevisiae were compared before and after mixing them for 90 minutes (i.e. allowing them to mate).
+  Keywords: yeast mating response, comparison among species
+:title: Mating response of three yeast species (S. cerevisiae, S. paradoxus and S. mikatae)
+:platform: GPL4567

data/install_scripts/GEO/series/GSE7537.yaml

@@ -0,0 +1,27 @@
+--- 
+:description: |-
+  Spontaneous mutations were accumulated in haploid strains of yeast. Expression profiling was performed on four MA lines and the ancestor in a complete loop design.
+  Keywords: Gene expression profiling
+:arrays: 
+  GSM182247: 
+    condition: MA-A1 MA-A4
+  GSM182248: 
+    condition: MA-A4 MA-A8
+  GSM182249: 
+    condition: MA-A8 MA-A3
+  GSM182250: 
+    condition: MA-A0 MA-A8
+  GSM182251: 
+    condition: MA-A8 MA-A1
+  GSM182252: 
+    condition: MA-A3 MA-A0
+  GSM182253: 
+    condition: MA-A3 MA-A1
+  GSM182244: 
+    condition: MA-A0 MA-A4
+  GSM182245: 
+    condition: MA-A4 MA-A3
+  GSM182246: 
+    condition: MA-A1 MA-A0
+:title: Mutation accumulation and the yeast transcriptome
+:platform: GPL5092

data/install_scripts/GEO/series/GSE7645.yaml

@@ -0,0 +1,152 @@
+--- 
+:description: |-
+  Oxidative stress is a harmful condition in a cell, tissue, or organ, caused by an imbalnace between reactive oxygen species and other oxidants and the capacity of antioxidant defense systems to remove them. The budding yeast S. cerevisiae has been the major eukaryotic model for studies of response to oxidative stress.
+  We used microarrays to study the genome-wide temporal response of the yeast S. cerevisiae to oxidative stress induced by cumene hydroperoxide.
+  Keywords: time course
+:arrays: 
+  GSM184988: 
+    time: "20"
+    condition: CHP
+  GSM184977: 
+    time: "3"
+    condition: CHP
+  GSM184966: 
+    time: "70"
+    condition: control
+  GSM184955: 
+    time: "12"
+    condition: control
+  GSM184944: 
+    time: "0"
+    condition: control
+  GSM184989: 
+    time: "40"
+    condition: CHP
+  GSM184978: 
+    time: "6"
+    condition: CHP
+  GSM184967: 
+    time: "120"
+    condition: control
+  GSM184956: 
+    time: "20"
+    condition: control
+  GSM184945: 
+    time: "3"
+    condition: control
+  GSM184990: 
+    time: "70"
+    condition: CHP
+  GSM184979: 
+    time: "12"
+    condition: CHP
+  GSM184968: 
+    time: "0"
+    condition: CHP
+  GSM184957: 
+    time: "40"
+    condition: control
+  GSM184946: 
+    time: "6"
+    condition: control
+  GSM184991: 
+    time: "120"
+    condition: CHP
+  GSM184980: 
+    time: "20"
+    condition: CHP
+  GSM184969: 
+    time: "3"
+    condition: CHP
+  GSM184958: 
+    time: "70"
+    condition: control
+  GSM184947: 
+    time: "12"
+    condition: control
+  GSM184981: 
+    time: "40"
+    condition: CHP
+  GSM184970: 
+    time: "6"
+    condition: CHP
+  GSM184959: 
+    time: "120"
+    condition: control
+  GSM184948: 
+    time: "20"
+    condition: control
+  GSM184982: 
+    time: "70"
+    condition: CHP
+  GSM184971: 
+    time: "12"
+    condition: CHP
+  GSM184960: 
+    time: "0"
+    condition: control
+  GSM184949: 
+    time: "40"
+    condition: control
+  GSM184983: 
+    time: "120"
+    condition: CHP
+  GSM184972: 
+    time: "20"
+    condition: CHP
+  GSM184961: 
+    time: "3"
+    condition: control
+  GSM184950: 
+    time: "70"
+    condition: control
+  GSM184984: 
+    time: "0"
+    condition: CHP
+  GSM184973: 
+    time: "40"
+    condition: CHP
+  GSM184962: 
+    time: "6"
+    condition: control
+  GSM184951: 
+    time: "120"
+    condition: control
+  GSM184985: 
+    time: "3"
+    condition: CHP
+  GSM184974: 
+    time: "70"
+    condition: CHP
+  GSM184963: 
+    time: "12"
+    condition: control
+  GSM184952: 
+    time: "0"
+    condition: control
+  GSM184986: 
+    time: "6"
+    condition: CHP
+  GSM184975: 
+    time: "120"
+    condition: CHP
+  GSM184964: 
+    time: "20"
+    condition: control
+  GSM184953: 
+    time: "3"
+    condition: control
+  GSM184987: 
+    time: "12"
+    condition: CHP
+  GSM184976: 
+    time: "0"
+    condition: CHP
+  GSM184965: 
+    time: "40"
+    condition: control
+  GSM184954: 
+    time: "6"
+    condition: control
+:title: Expression data for Saccharomyces cerevisiae oxidative stress response
+:platform: GPL90

data/install_scripts/GEO/series/GSE7660.yaml

@@ -0,0 +1,41 @@
+--- 
+:description: |-
+  The Target Of Rapamycin (TOR) protein is a Ser/Thr kinase that functions in two distinct multiprotein complexes: TORC1 and TORC2. These conserved complexes regulate many different aspects of cell growth in response to intra- and extracellular cues. Here we report the first bona fide substrate of yeast TORC1: the AGC-kinase Sch9. Six amino acids in the c-terminus of Sch9 are directly phosphorylated by TORC1. Phosphorylation of these residues is lost upon rapamycin-treatment as well as carbon- or nitrogen-starvation and transiently reduced following application of osmotic, oxidative or thermal stress. TORC1-dependent phosphorylation is required for Sch9 activity and replacement of residues phosphorylated by TORC1 with Asp/Glu renders Sch9 activity TORC1-independent. Sch9 is required for TORC1 to properly regulate ribosome biogenesis, translation initiation and entry into G0 phase, but not expression of Gln3-dependent genes. Our results suggest that Sch9 functions analogously to the mammalian TORC1 substrate S6K1 rather than the mTORC2 substrate PKB/Akt.
+  Keywords: time course, cell type.
+:arrays: 
+  GSM185501: 
+    condition: CEN_SCH9(WT)_Rapamycin_20min
+  GSM185502: 
+    condition: CEN_SCH9(WT)_Rapamycin_30min
+  GSM185514: 
+    condition: CEN_SCH9(WT)_Rapamycin_60min
+  GSM185503: 
+    condition: CEN_Rapamycin_120min
+  GSM185515: 
+    condition: CEN_SCH9(WT)_Rapamycin_90min
+  GSM185504: 
+    condition: CEN_Rapamycin_180min
+  GSM185516: 
+    condition: CEN_SCH9(WT)_Rapamycin_120min
+  GSM185505: 
+    condition: CEN_SCH9(2D3E)_Rapamycin_90min
+  GSM185517: 
+    condition: CEN_SCH9(WT)_Rapamycin_180min
+  GSM185506: 
+    condition: CEN_SCH9(2D3E)_Rapamycin_120min
+  GSM185518: 
+    condition: CEN_Rapamycin_60min
+  GSM185507: 
+    condition: CEN_SCH9(2D3E)_Rapamycin_180min
+  GSM185519: 
+    condition: CEN_Rapamycin_90min
+  GSM185035: 
+    condition: CEN_Rapamycin_20min
+  GSM185498: 
+    condition: CEN_Rapamycin_30min
+  GSM185499: 
+    condition: CEN_SCH9(2D3E)_Rapamycin_20min
+  GSM185500: 
+    condition: CEN_SCH9(2D3E)_Rapamycin_30min
+:title: Sch9 Is a Major Target of TORC1 in Saccharomyces cerevisiae
+:platform: GPL884

data/install_scripts/GEO/series/GSE7820.yaml

@@ -0,0 +1,30 @@
+--- 
+:arrays: 
+  GSM189736: 
+    treatment: MLY132_YPM
+  GSM189737: 
+    treatment: MLY132_SLAM
+  GSM189738: 
+    treatment: MLY61_YPM
+  GSM189739: 
+    treatment: MLY61_SLAM
+  GSM189740: 
+    treatment: MLY61_YPM
+  GSM189741: 
+    treatment: MLY61_SLAM
+  GSM189742: 
+    treatment: MLY61_YPM
+  GSM189743: 
+    treatment: MLY61_SLAM
+  GSM189732: 
+    treatment: MLY132_YPM
+  GSM189733: 
+    treatment: MLY132_SLAM
+  GSM189734: 
+    treatment: MLY132_YPM
+  GSM189735: 
+    treatment: MLY132_SLAM
+:description: "In response to limited nitrogen and abundant carbon sources, diploid Saccharomyces cerevisiae strains undergo a filamentous transition in cell growth as part of pseudohyphal differentiation. Use of the disaccharide maltose as the principal carbon source, in contrast to the preferred nutrient monosaccharide glucose, has been shown to induce a hyper-filamentous growth phenotype in a strain deficient for GPA2 which codes for a G\xEF\x81\xA1 protein component that interacts with the glucose-sensing receptor Gpr1p to regulate filamentous growth. In this report, we compare the global transcript and proteomic profiles of wild-type and Gpa2p deficient diploid yeast strains grown on both rich and nitrogen starved maltose media. We find that deletion of GPA2 results in significantly different transcript and protein profiles when switching from rich to nitrogen starvation media.  The results are discussed with a focus on the genes associated with carbon utilization, or regulation thereof, and a model for the contribution of carbon sensing/metabolism-based signal transduction to pseudohyphal differentiation is proposed.\n\
+  Keywords: Saccharomyces cerevisiae, nitrogen starvation, maltose, pseudohyphal differentiation, yeast, expression profiling"
+:title: Transcript and Proteomic Analyses of Wild-Type and GPA2 Mutant Saccharomyces cerevisiae Strains
+:platform: GPL90

data/install_scripts/GEO/series/GSE79.yaml

@@ -0,0 +1,32 @@
+--- 
+:title: Lager beer fermentation time course
+:description: |-
+  The dynamics of the Saccharomyces carlsbergensis brewing yeast transcriptome during a production scale lager beer fermentation.
+  The transcriptome of a lager brewing yeast (Saccharomyces carlsbergensis, syn. of S. pastorianus), was analysed at 12 different time points spanning a production-scale lager beer fermentation. Generally, the average expression rapidly increased and had a maximum value on day 2, then decreased as the sugar got consumed. Especially genes involved in protein and lipid biosynthesis or glycolysis were highly expressed during the beginning of the fermentation. Similarities as well as significant differences in expression profiles could be observed when comparing to a previous transcriptome analysis of a laboratory yeast grown in YPD. The regional distribution of various expression levels on the chromosomes appeared to be random or near-random and no reduction in expression near telomeres was observed.
+  Keywords: time-course
+:arrays: 
+  GSM2375: 
+    condition: ferm96h
+  GSM2376: 
+    condition: ferm120h
+  GSM2377: 
+    condition: ferm144h
+  GSM2378: 
+    condition: ferm168h
+  GSM2380: 
+    condition: ferm240h
+  GSM2379: 
+    condition: ferm182h
+  GSM2381: 
+    condition: ferm264h
+  GSM2370: 
+    condition: ferm0h
+  GSM2371: 
+    condition: ferm1h
+  GSM2372: 
+    condition: ferm24h
+  GSM2373: 
+    condition: ferm48h
+  GSM2374: 
+    condition: ferm72h
+:platform: GPL205

data/install_scripts/GEO/series/GSE8035.yaml

@@ -0,0 +1,19 @@
+--- 
+:description: |-
+  Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified.
+  Keywords: Chemostat-based transcriptome analysis
+:arrays: 
+  GSM198364: 
+    condition: Zinc limited Aerobic
+  GSM198365: 
+    condition: Zinc limited Aerobic
+  GSM198366: 
+    condition: Zinc limited Aerobic
+  GSM198367: 
+    condition: Zinc-limited Anaerobic
+  GSM198368: 
+    condition: Zinc-limited Anaerobic
+  GSM198369: 
+    condition: Zinc-limited Anaerobic
+:title: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures
+:platform: GPL90

data/install_scripts/GEO/series/GSE8088.yaml

@@ -0,0 +1,13 @@
+--- 
+:description: |-
+  Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified
+  Keywords: Chemostat-based transcriptome analysis
+:arrays: 
+  GSM200685: 
+    condition: Carbon-limited Aerobic
+  GSM200686: 
+    condition: Carbon-limited Aerobic
+  GSM200687: 
+    condition: Carbon-limited Aerobic
+:title: Transcriptional responses of Saccharomyces cerevisiae to carbon limitation in aerobic chemostat cultures
+:platform: GPL90

data/install_scripts/GEO/series/GSE8089.yaml

@@ -0,0 +1,19 @@
+--- 
+:description: |-
+  Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified
+  Keywords: Chemostat based transcriptome analysis
+:arrays: 
+  GSM200693: 
+    condition: Nitrogen-limited Anaerobic
+  GSM200688: 
+    condition: Nitrogen-limited Aerobic
+  GSM200690: 
+    condition: Nitrogen-limited Aerobic
+  GSM200689: 
+    condition: Nitrogen-limited Aerobic
+  GSM200691: 
+    condition: Nitrogen-limited Anaerobic
+  GSM200692: 
+    condition: Nitrogen-limited Anaerobic
+:title: Trasncriptional response of Saccharomyces cerevisiae to nitrogen limitation in chemostat culture
+:platform: GPL90

data/install_scripts/GEO/series/GSE8111.yaml

@@ -0,0 +1,15 @@
+--- 
+:description: |-
+  In Saccharomyces cerevisiae, the Gcn2p kinase controls a gene expression program in response to nutrient deprivation. Upon amino acid deprivation Gcn2p phosphorylates the translation initiation factor 2a subunit (eIF2a). Phosphorylation of eIF2a  transiently inhibits translation initiation, and favours selective translation of the GCN4 transcription factor mRNA. High levels of Gcn4p then activate the expression of genes encoding amino acid biosynthesis pathways. Besides nutrient deprivation, Gcn2p can also be activated by other stresses such as DNA damage. Previous studies in our lab suggested that Gcn2p regulated other cellular pathways apart from translation initiation. To gain insights into these new regulatory roles of Gcn2p, we generated a strain called (GCN2c) expressing a constitutively active Gcn2p kinase mutant. In the GCN2c strain, phosphorylation of eIF2a and translation of a GCN4-lacz reporter was constitutively high in the absence of amino acid starvation. We investigated the transcriptional profile of the GCN2c mutant strain by cDNA microarrays. As expected, numerous amino acid biosynthetic genes were upregulated, being dependent of Gcn4p. Most interestingly, expression of genes encoding proteins involved in DNA replication/repair was decreased, suggesting that Gcn2p could regulate cell cycle progression from G1 to S phase. Accordingly, the Gcn2c strain exhibited, i) slow growth, ii) a delayed entry into S phase, and iii) hypersensitivity to hydroxyurea. In addition, MMS treatment induced a G1 checkpoint and a growth defect which was dependent on Gcn2p and Gcn3p. Considering that MMS delays cell cycle progression by generating DNA lesions, the findings suggest that DNA damage induces a G1/S checkpoint by a novel pathway involving the protein kinase Gcn2p.
+  Keywords: mutant analysis
+:arrays: 
+  GSM194695: 
+    condition: WT vs GCN2
+  GSM194696: 
+    condition: WT vs GCN2
+  GSM194697: 
+    condition: WT vs GCN2
+  GSM194393: 
+    condition: WT vs GCN2
+:title: Gcn2p regulates a G1/S cell cycle checkpoint in response to DNA damage
+:platform: GPL4069

data/install_scripts/GEO/series/GSE8237.yaml

@@ -0,0 +1,35 @@
+--- 
+:description: |-
+  The cellular response to treatment with DNA-damaging substances at low concentrations which are genotoxic but do not have a strong cytotoxic effect are of special interest. In addition, environmental variations that influence growth conditions, e.g. different media, and individual fitness, e.g. different strains, are likely to influence and modulate the adverse effects of individual DNA damaging substances. At sub-cytotoxic levels, DNA damaging substances play an important role in the accumulation of genomic mutations. In longer living organisms, like humans and other mammals, exposure to DNA damaging substances over extended period of time is a critical factor that contributes to the development of various diseases and in particular of tumors. The aim of our work was to study how strain background and growth conditions influence respond to DNA damage caused by low doses of MMS and which part of these changes is responsible for their sensitivity to toxic conditions. We analyzed sensitivity of two yeast strains FF18984 and BY4742 to MMS in media with limited and full nutrient availability.
+  Keywords: Yeast, S.cerevisiae, MMS, stress response, DNA damage
+:arrays: 
+  GSM203849: 
+    condition: BY4742 strain, YPD medium, mock-treated, 1h
+  GSM202808: 
+    condition: YPD medium, mock-treated, 1h
+  GSM202797: 
+    condition: F1 medium, 0.0125 MMS, 30 min
+  GSM202764: 
+    condition: F1 medium, mock-treated, 30 min
+  GSM203852: 
+    condition: BY4742 strain, YPD medium, 0.0125 MMS, 1h
+  GSM202809: 
+    condition: YPD medium, 0.00125 MMS, 1h
+  GSM202765: 
+    condition: F1 medium, 0.00125 MMS, 30 min
+  GSM202810: 
+    condition: YPD medium, 0.0125 MMS, 1h
+  GSM202799: 
+    condition: F1 medium, mock-treated, 1h
+  GSM202801: 
+    condition: F1 medium, 0.00125 MMS, 1h
+  GSM202802: 
+    condition: F1 medium, 0.0125 MMS, 1h
+  GSM202803: 
+    condition: YPD medium, mock-treated, 30 min
+  GSM202804: 
+    condition: YPD medium, 0.00125 MMS, 30 min
+  GSM202805: 
+    condition: YPD medium, 0.0125 MMS, 30 min
+:title: Low-level MMS treatment of S.cerevisiae
+:platform: GPL5398