Discovery and validation of Barrett's esophagus microRNA transcriptome by next generation sequencing.

ABSTRACT:

Objective

Barrett's esophagus (BE) is transition from squamous to columnar mucosa as a result of gastroesophageal reflux disease (GERD). The role of microRNA during this transition has not been systematically studied.

Design

For initial screening, total RNA from 5 GERD and 6 BE patients was size fractionated. RNA <70 nucleotides was subjected to SOLiD 3 library preparation and next generation sequencing (NGS). Bioinformatics analysis was performed using R package "DEseq". A p value<0.05 adjusted for a false discovery rate of 5% was considered significant. NGS-identified miRNA were validated using qRT-PCR in an independent group of 40 GERD and 27 BE patients. MicroRNA expression of human BE tissues was also compared with three BE cell lines.

Results

NGS detected 19.6 m

SUBMITTER: Bansal A 

PROVIDER: S-EPMC3553128 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature