Project PXD000276

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Summary

Title

Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells

Description

Data on absolute molecule numbers will empower the modeling, understanding, and comparison of cellular functions and biological systems. We quantified transcriptomes and proteomes in fission yeast during cellular proliferation and quiescence. This rich resource provides the first comprehensive reference for all RNA and most protein concentrations in a eukaryote under two key physiological conditions. The integrated data set supports quantitative biology and affords unique insights into cell regulation. Although mRNAs are typically expressed in a narrow range above 1 copy/cell, most long, noncoding RNAs, except for a distinct subset, are tightly repressed below 1 copy/cell. Cell-cycle-regulated transcription tunes mRNA numbers to phase-specific requirements but can also bring about more switch-like expression. Proteins greatly exceed mRNAs in abundance and dynamic range, and concentrations are regulated to functional demands. Upon transition to quiescence, the proteome changes substantially, but, in stark contrast to mRNAs, proteins do not uniformly decrease but scale with cell volume. Proteomics data generation and processing: Extracted proteins were enzymatically digested using trypsin, the peptides were separated into 12 fractions using an OFF-GEL Fractionator (Agilent), and analyzed on an Orbitrap Velos LC-MS platform (Thermo Scientific). Peptides were quantified and identified using the Progenesis LC-MS (Nonlinear Dynamics) and Mascot software, respectively. Absolute abundance for 39 proteins was determined using spiked-in heavy reference peptides to translate the summed MS-intensities of all peptides to copies/cell for all identified proteins. The associated microarray and RNA-seq datasets are in ArrayExpress with the following accession numbers: Microarrays: E-TABM-1075, RNA-seq: E-MTAB-1154.

Sample Processing Protocol

See details in reference(s) : 23101633

Data Processing Protocol

See details in reference(s) : 23101633

Contact

Alexander Schmidt, Proteomics Core Facility

Submission Date

05/06/2013

Publication Date

06/06/2013

Publication

    Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bähler J; Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells., Cell, 2012 Oct 26, 151, 3, 671-83, PubMed: 23101633

Assay

Showing 1 - 1 of 1 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 29627 proliferating cells 9101 173994 37236 162549 162549