©The Author(s) 2017. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Nov 7, 2017; 23(41): 7369-7386
Published online Nov 7, 2017. doi: 10.3748/wjg.v23.i41.7369
Published online Nov 7, 2017. doi: 10.3748/wjg.v23.i41.7369
Parallel mRNA, proteomics and miRNA expression analysis in cell line models of the intestine
Finbarr O’Sullivan, Joanne Keenan, Sinead Aherne, Fiona O’Neill, Michael Henry, Paula Meleady, Laura Breen, Niall Barron, Martin Clynes, Padraig Doolan, National Institute for Cellular Biotechnology, Dublin City University, Dublin D09 W6Y4, Ireland
Colin Clarke, National Institute for Bioprocessing Research & Training, Blackrock, Dublin A94 X099, Ireland
Karina Horgan, Richard Murphy, Alltech, Dunboyne, Meath, A86 X006, Ireland
Author contributions: O'Sullivan F was involved at all stages of the research and co-wrote the manuscript; Doolan P coordinated the analysis of the triomic dataset and co-wrote the manuscript; Keenan J and Breen L performed the cell culture and prepared samples for analysis; Aherne S and O’Neill F performed the microarray experiments; Henry M and Meleady P performed the proteomic experiments; Clarke C and Barron N performed bioinformatics analysis on the data; Murphy R designed and coordinated the research programme with help from Clynes M and Horgan K; All authors read and reviewed the manuscript; Doolan P and Murphy R contributed equally to this work and are joint-last Authors.
Supported by A Strategic Alliance Programme between Alltech Ltd. and DCU and also Enterprise Ireland Innovation Partnership Grant (IP 2015 0375).
Conflict-of-interest statement: The authors declare they have no conflicts of interest.
Data sharing statement: All data generated or analysed during this study are included in this published article and its supplementary information files.
Correspondence to: Finbarr O’Sullivan, PhD, Associate Director, National Institute for Cellular Biotechnology, Dublin City University, Dublin D09 W6Y4, Ireland. finbarr.osullivan@dcu.ie
Telephone: +353-1-7005700
Received: May 16, 2017
Peer-review started: May 18, 2017
First decision: June 22, 2017
Revised: July 7, 2017
Accepted: August 8, 2017
Article in press: August 8, 2017
Published online: November 7, 2017
Processing time: 173 Days and 13.9 Hours
Peer-review started: May 18, 2017
First decision: June 22, 2017
Revised: July 7, 2017
Accepted: August 8, 2017
Article in press: August 8, 2017
Published online: November 7, 2017
Processing time: 173 Days and 13.9 Hours
Core Tip
Core tip: Unique triomics analysis of Caco-2 and HT-29, two commonly used in vitro cell lines models of the intestine, was conducted. This analysis not only provided data on differentially expressed mRNAs, miRNAs and proteins but also allowed the identification of miRNA-regulated proteins differentially expressed between these two cell lines.