Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
T.T
Primary Tissue
Esophagus
Tissue Diagnosis
Carcinoma Squamous Cell

Attributes by original data submitter

Sample

source_name
TT_input
cell lines
TT
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinked with 1% formaldehyde, washed with PBS, lysed in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), sonicated with Covaris E210 to shear DNA to 200-1500bp. After immunoprecipitation or without immunoprecipitation for input, beads were washed, RNase A and Proteinase K treated and reverse crosslinked in elution buffer (1% SDS, 0.1M NaHCO3). DNAs were column purified and subjected to standard Illumina library construction.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
25570266
Reads aligned (%)
99.4
Duplicates removed (%)
2.3
Number of peaks
853 (qval < 1E-05)

hg19

Number of total reads
25570266
Reads aligned (%)
98.3
Duplicates removed (%)
4.0
Number of peaks
982 (qval < 1E-05)

Base call quality data from DBCLS SRA