PXD000678

PXD000678 is an original dataset announced via ProteomeXchange.

Title	A Proteomic Chronology of Gene Expression through the Cell Cycle in Human Myeloid Leukemia Cells.
Description	Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over ~6,000 genes individually across the cell cycle, revealing complex, gene-specific patterns. This dataset, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:48:56.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vackar Afzal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue; oxidized residue; phosphorylated residue; Acetyl; methylated lysine; N-acylated residue; methylated arginine; 2-pyrrolidone-5-carboxylic acid (Gln)
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-01-09 06:32:08	ID requested
1	2014-03-12 07:28:33	announced
⏵ 2	2014-07-24 03:48:57	announced	Updated project metadata.

Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, Stratton MR, Lamond AI, A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. Elife, 3():e01630(2014) [pubmed]

curator keyword: Biological

submitter keyword: Cell Cycle, FASP, hSAX, Human, NB4

Prof Angus Lamond
contact affiliation	College of Life Sciences, University of Dundee
contact email	a.i.lamond@dundee.ac.uk
lab head
Vackar Afzal
contact affiliation	School of Life Sciences
contact email	v.z.afzal@dundee.ac.uk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/03/PXD000678

PRIDE project URI

• PRIDE
  1. PXD000678
     1. Label: PRIDE project
     2. Name: A Proteomic Chronology of Gene Expression through the Cell Cycle in Human Myeloid Leukemia Cells.