E-MTAB-1398 - Transcription profiling by tiling array of Saccharomyces cerevisiae strains grown in four media to investigate pathways mediating genetic signals to phenotype

Status
Last updated on 12 August 2013, released on 12 August 2013
Organism
Saccharomyces cerevisiae
Samples (135)
Array (1)
Protocols (5)
Description
Unraveling the causal chain of biochemical events that link genotype to phenotype is critical for understanding the molecular basis of genetic diseases and for designing personalized drug therapies. To this end, using yeast as a model system, we carried out joint profiling of fitness and gene expression. Transcription profile includes 4 media (YPD (YPE, YPMalt, YPE and YPD_BPS) of ~35 segregants spores each media were obtained from a cross of the yeast strains S96 and YJM789. These spores are a subset of those published by Mancera et al, Nature, 2008. Sufficient cells were grown at 30 °C in media of interest to the mid log phase. After harvest, gene expression profiling were performed using tiling array as previous described (Xu et al, Nature, 2009). The expression level of each transcript was used as molecular trait for further investigation in the study. 1 CEL data files was mislabelled: 110427_09C_BPS_(Scerevisiae_tlg).CEL.gz, actually spores 09D. The correct spore IDs are in the sample annotation (under StrainOrLine or sample name).
Experiment types
transcription profiling by tiling array, co-expression, growth condition, individual genetic characteristics, transcript identification
Contact
Citations
Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype. Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon A, Peer D, Steinmetz LM. PLoS Genet 9(9) (2013)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MTAB-1398.idf.txt
Sample and data relationshipE-MTAB-1398.sdrf.txt
Raw data (16)Click to browse raw data
Array designA-AFFY-116.adf.txt
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