Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Digestive tract

Cell type

Barrett Esophagus

MeSH Description

A condition with damage to the lining of the lower ESOPHAGUS resulting from chronic acid reflux (ESOPHAGITIS, REFLUX). Through the process of metaplasia, the squamous cells are replaced by a columnar epithelium with cells resembling those of the INTESTINE or the salmon-pink mucosa of the STOMACH. Barrett's columnar epithelium is a marker for severe reflux and precursor to ADENOCARCINOMA of the esophagus.

Sample

ENA first public

2018-09-24

ENA last update

2018-05-01

ENA-CHECKLIST

ERC000011

External Id

SAMEA4625053

INSDC center alias

UOM

INSDC center name

University of Manchester

INSDC first public

2018-09-24T17:02:04Z

INSDC last update

2018-05-01T11:22:28Z

INSDC status

public

Submitter Id

E-MTAB-6751:B_003

broker name

ArrayExpress

common name

human

disease

Barrett's esophagus

individual

3

organism part

esophagus

sample name

E-MTAB-6751:B_003

Sequenced DNA Library

library_name

B_003_p

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Barrett's oesophagus biopsies were collected from routine endoscopies and placed into PBS on ice. Biopsies were minced with a scalpel and lysed in ATAC lysis buffer and Tn5 reactions were performed as described in Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba, Howard Y. Chang and William J. Greenleaf. doi:10.1038/nmeth.2688 Libraries were constructed by amplifying transposed DNA with Illumina Nextera adapters

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

44650705

Reads aligned (%)

97.5

Duplicates removed (%)

12.1

Number of peaks

6473 (qval < 1E-05)

hg19

Number of total reads

44650705

Reads aligned (%)

97.0

Duplicates removed (%)

12.3

Number of peaks

6363 (qval < 1E-05)