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Title: RNA-seq of gastric biopsies from subjects at different stages of gastric inflammation and histological changes      
dateReleased:
12-31-2015
description:
In this study we performed RNA-seq analysis of gastric corpus biopsies to study transcriptional changes during early gastric carcinogenesis. We included patients with non-atrophic gastritis, with intermediate and extensive corpus atrophy, and patients with intestinal metaplasia. We also included a control group of H. pylori-negative subjects. All subjects were from Nicaragua, which has a population of high gastric cancer risk. Total RNA samples were treated with RiboZero Magnetic (Human/Mouse/Rat) Kit (Epicentre Biotechnologies) to deplete rRNA and the cDNA libraries were prepared using ScriptSeqTM v2 RNA-Seq Library Preparation Kit (Epicentre). Sequencing was performed on the Illumina HiScan2500 platform, 2*100bp reads.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-MTAB-3689
refinement:
raw
dateSubmitted:
06-11-2012
keywords:
functional genomics
dateModified:
06-30-2015
creators:
Kaisa Thorell
availability:
available
types:
gene expression
name:
Homo sapiens
name:
observational design
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-3689/E-MTAB-3689.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-3689/E-MTAB-3689.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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