Illumina HiSeq 2500 sequencing; GSM1335531: RME1O_RSF1O_IME1cO_IME1ncO - Repl 1; Saccharomyces cerevisiae; RNA-Seq

RME1O_RSF1O_IME1cO_IME1ncO - Repl 1

We study the effect of four QTN in RME1, IME1 & RSF1 that are causative for variation in sporulation efficiency. We investigate the relationship between genotype, gene expression and phenotype and whether the amount of gene expression variation explained by the sporulation QTN is predictive of the amount of phenotypic variation explained by them. Overall design: RNA-Seq analysis of 4 replicates each of 16 allele replacement panel strains containing all combinations of the four sporulation QTN after 2 hours in sporulation medium.

Gene expression profiling in allele replacement panel strains containing all combinations of four sporulation QTN in S. cerevisiae

Submitted by Gene Expression Omnibus on 03-JUN-2014

Total RNA was extracted using standard procedures. mRNA was extracted with the DynaI mRNA DIRECTâ„¢ kit (Life Technologies) and fragmented with a Covaris Focused ultrasonicator. mRNA extraction and fragmentation, random hexamer priming of cDNA and Illumina library preparations were done using standard procedures. Illumina libraries were prepared from the cDNA of each of the 64 samples. We obtained libraries from all the samples except the strain with vineyard alleles of RME1nc, RSF1c, IME1nc and oak allele of IME1c which had only 3 replicates for the subsequent analyses. The libraries were indexed separately and pooled into one sequencing reaction. The pool was run on multiple lanes until we obtained a minimum of 4 million reads per sample. The sequencing reads from each run were de-multiplexed before sequencing reads from each sample were processed independently. The sequencing reads for each sample were combined across all sequencing runs before data processing.

Gene expression profiling in allele replacement panel strains containing all combinations of four sporulation QTN in S. cerevisiae

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