PXD001533

PXD001533 is an original dataset announced via ProteomeXchange.

Title	Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with acid guanidinium thiocyanate-phenol-chloroform
Description	Acid guanidinium thiocyanate, phenol and chloroform extraction (AGPC) is a commonly used procedure to extract RNA from fresh frozen tissues and cell lines. In addition, DNA and proteins can be recovered, which makes AGPC an attractive source for integrative analysis on tissues of which little material is available, such as clinical specimens. Despite this potential, AGPC has only scarcely been used for proteomic analysis, mainly due to difficulties in extracting proteins. We have used a quantitative mass spectrometry method to show that proteins can readily be recovered from AGPC extracted tissues with high recovery and repeatability, which allows this method to be used for global proteomic profiling. Protein expression data for a selected number of clinically relevant markers, of which transcript and protein levels are known to be correlated, was in agreement with genomic and transcriptomic data obtained from the same AGPC lysate. Furthermore, global proteomic profiling successfully discriminated breast tumor tissues according to their clinical subtype. Lastly, a reference gene set of differentially expressed transcripts was strongly enriched in the differentially abundant proteins in our cohort. AGPC lysates are therefore well suited for comparative protein and integrative analyses.
HostingRepository	PRIDE
AnnounceDate	2016-06-24
AnnouncementXML	Submission_2016-06-24_11:34:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rene Braakman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-11-24 06:45:02	ID requested
⏵ 1	2016-06-24 11:34:33	announced

Braakman RB, Bezstarosti K, Sieuwerts AM, de Weerd V, van Galen AM, Stingl C, Luider TM, Timmermans MA, Smid M, Martens JW, Foekens JA, Demmers JA, Umar A, Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with acid guanidinium thiocyanate-phenol-chloroform. J Proteome Res, 14(3):1627-36(2015) [pubmed]

curator keyword: Biomedical, Technical

submitter keyword: breast cancer, proteogenomics, sample preparation, RNA Bee, acid guanidinium phenol-chloroform, shotgun proteomics

Prof. Dr. J.A. Foekens
contact affiliation	Erasmus MC, dept. Medical Oncology, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
contact email	j.foekens@erasmusmc.nl
lab head
Rene Braakman
contact affiliation	Erasmus MC, Department of Medical Oncology, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
contact email	r.braakman@erasmusmc.nl
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/2016/06/PXD001533

PRIDE project URI

• PRIDE
  1. PXD001533
     1. Label: PRIDE project
     2. Name: Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with acid guanidinium thiocyanate-phenol-chloroform