Optimisation of laboratory methods for whole transcriptomic RNA analyses in human left ventricular biopsies and blood samples of clinical relevance

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Title: Optimisation of laboratory methods for whole transcriptomic RNA analyses in human left ventricular biopsies and blood samples of clinical relevance
Authors: Ford, KL
Anwar, M
Heys, R
Ahmed, EM
Caputo, M
Game, L
Reeves, BC
Punjabi, PP
Angelini, GD
Petretto, E
Emanueli, C
Item Type: Journal Article
Abstract: This study aimed to optimise techniques for whole transcriptome and small RNA analyses on clinical tissue samples from patients with cardiovascular disease. Clinical samples often represent a particular challenge to extracting RNA of sufficient quality for robust RNA sequencing analysis, and due to availability, it is rarely possible to optimise techniques on the samples themselves. Therefore, we have used equivalent samples from pigs undergoing cardiopulmonary bypass surgery to test different protocols for optimal RNA extraction, and then validated the protocols in human samples. Here we present an assessment of the quality and quantity of RNA obtained using a variety of commercially-available RNA extraction kits on both left ventricular biopsies and blood plasma. RNA extraction from these samples presents different difficulties; left ventricular biopsies are small and fibrous, while blood plasma has a low RNA content. We have validated our optimised extraction techniques on human clinical samples collected as part of the ARCADIA (Association of non-coding RNAs with Coronary Artery Disease and type 2 Diabetes) cohort study, resulting in successful whole transcriptome and small RNA sequencing of human left ventricular tissue.
Issue Date: 14-Mar-2019
Date of Acceptance: 18-Feb-2019
URI: http://hdl.handle.net/10044/1/67995
DOI: https://dx.doi.org/10.1371/journal.pone.0213685
ISSN: 1932-6203
Publisher: Public Library of Science (PLoS)
Journal / Book Title: PLoS ONE
Volume: 14
Issue: 3
Copyright Statement: © 2019 Ford et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Sponsor/Funder: British Heart Foundation
Funder's Grant Number: FMDY1548246 (ORCA #56436)
Keywords: MD Multidisciplinary
General Science & Technology
Publication Status: Published
Conference Place: United States
Article Number: e0213685
Appears in Collections:Clinical Sciences
National Heart and Lung Institute
Molecular Sciences
Faculty of Medicine

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