RNA-seq of chemostat grown yeast (Y11335 BY4742 )

We profiled total-mRNA from yeast cells grown in identical conditions to match samples submitted for proteome-wide absolute quantification. Matching mRNA profiles to absolute protein copies numbers enables a more accurate comparison of transcript to final protein levels. Here we were able to show direct comparison results in a correlation of Rsquared of 0.58, show suggesting as much as ~40% of final protein levels in yeast cannot be determined from mRNA levels alone. Reads were mapped to a reference genome of S. cerevisiae, downloaded from the Saccharomyces Genome Database (SGD), using Bowtie version 1 (74). Mapped sequences were then assembled into transcripts and quantified using Cufflinks version 2.0 (75) (using the SGD reference genome GTF file). Overall design: mRNA profile of 4 biological replicates of S.cerevisiae to match quantitative analysis of the proteome