PXD000276

PXD000276 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2013-06-10
AnnouncementXML	Submission_2013-06-10_03:21:08.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000276
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Schizosaccharomyces pombe (Fission yeast); NCBI TaxID: 4896;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; neutral loss: 63.998285; acetylated residue
Instrument	radial ejection linear ion trap

Revision	Datetime	Status	ChangeLog Entry
0	2013-06-05 02:25:56	ID requested
1	2013-06-06 05:21:03	announced
1	2014-07-28 00:39:00	announced
⏵ 2	2013-06-10 03:21:08	announced	Add reference

Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, B, ä, hler J, Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell, 151(3):671-83(2012) [pubmed]

submitter keyword: S. pombe, fission yeast, absolute protein quantification

Alexander Schmidt
contact affiliation	Proteomics Core Facility
contact email	alex.schmidt@unibas.ch

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• PRIDE
  1. 29627
     1. InstrumentRef: INSTRUMENT_1
     2. Label: S. pombe proteins
     3. ModificationList: monohydroxylated residue, iodoacetamide derivatized residue, neutral loss, acetylated residue,
     4. Name: proliferating cells
     5. PublicationRef: PMID23101633