Computational protocol: The yeast osmostress response is carbon source dependent

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Protocol publication

[…] Strain W303-1A was employed. RNA from the biomass samples was extracted and purified using Qiagen RNeasy Mini Kit extraction and DNA degradation according to the user’s manual (Qiagen, Hilden, Germany). Integrity of the product was verified using 2100 Bioanalyzer instrument according to its user’s manual (Agilent Technologies, Santa Clara, US). RNA concentration was determined by a NanoDrop 2000 (Thermo Scientific, Wilmington, USA). The Illumina TruSeq sample preparation kit v2, with poly-A selection, was used to prepare RNA samples for sequencing. Fragments were clustered on cBot and sequenced on two lanes on an Illumina HiSeq 2500 with paired ends (2 × 100 bp), according to the manufacturer’s instructions. The short reads were mapped to the W303 reference genome using TopHat version 2.0.10. Each sample had between 11.4 to 16.4 million mappable reads, with an average map rate of 91.2%. Read counts were determined using the featureCounts software from the subread package, version 1.4.0-p1. FPKM-values were calculated using Cufflinks version 2.1.1. Read counts were used in the differential expression analysis, with the software DESeq. P-values were adjusted for multiple testing using the Benjamini–Hochberg procedure as implemented in DESeq. All conditions were compared to the reference sample. Raw data from the experiments were deposited in ArrayExpress and assigned the identifier E-MTAB-5213. […]

Pipeline specifications

Software tools TopHat, Subread, Cufflinks, DESeq
Databases ArrayExpress
Application WES analysis
Organisms Saccharomyces cerevisiae
Diseases Substance-Related Disorders
Chemicals Ethanol, Carbon, Glucose, Glycerol, Trehalose