Dataset Information

Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with acid guanidinium thiocyanate-phenol-chloroform

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap, Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Prof. Dr. J.A. Foekens

PROVIDER: MSV000080789 | MassIVE | Wed Mar 29 15:18:00 BST 2017

SECONDARY ACCESSION(S): PXD001533

REPOSITORIES: MassIVE

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Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with acid guanidinium thiocyanate-phenol-chloroform.

Braakman René B H RB Bezstarosti Karel K Sieuwerts Anieta M AM de Weerd Vanja V van Galen Anne M AM Stingl Christoph C Luider Theo M TM Timmermans Mieke A M MA Smid Marcel M Martens John W M JW Foekens John A JA Demmers Jeroen A A JA Umar Arzu A

Journal of proteome research 20150202 3

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 quantit ...[more]

PMID: 25611981

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