Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

Tue Bjerg Bennike; Kenneth Kastaniegaard; Simona Padurariu; Michael Gaihede; Svend Birkelund; Vibeke Andersen; Allan Stensballe

Data in Brief (Mar 2016)

Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

Tue Bjerg Bennike,
Kenneth Kastaniegaard,
Simona Padurariu,
Michael Gaihede,
Svend Birkelund,
Vibeke Andersen,
Allan Stensballe

Affiliations

Tue Bjerg Bennike: Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark; Department of Health Science and Technology, Aalborg University, Aalborg, Denmark; Corresponding author. Tel.: +45 2613 9003.
Kenneth Kastaniegaard: Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
Simona Padurariu: Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
Michael Gaihede: Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
Svend Birkelund: Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
Vibeke Andersen: Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark; Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark.
Allan Stensballe: Department of Health Science and Technology, Aalborg University, Aalborg, Denmark

Journal volume & issue: Vol. 6
pp. 942 – 947

Abstract

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Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control (“Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples” [1]). We here report the data from the analysis. The comparative analysis was performed on 24 colon mucosa biopsies, extracted from the sigmoideum of two gastroenterologically healthy participants for the purpose of this study. A set of biopsies were additionally stored for 30 min at room temperature prior to formalin-fixation. The samples were analyzed by high throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002029. Keywords: Human, Colon, Mucosa, RNAlater, FFPE, Snap-frozen, Stability, LC–MS, Proteomics

Published in Data in Brief

ISSN: 2352-3409 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Medicine: Medicine (General): Computer applications to medicine. Medical informatics; Science: Science (General)
Website: http://www.journals.elsevier.com/data-in-brief/

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