Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EBF1

Cell type

Cell type Class
Digestive tract
Cell type
Hs 746.T
NA
NA

Attributes by original data submitter

Sample

source_name
gastric cancer cell line
cell line
HS746T
cell type
gastric cancer cell line
chip antibody
EBF1 (Santa Cruz Biotechnology, sc-137065)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
30 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and reactions were stopped by adding glycine to a final concentration of 0.2 M. Chromatin was extracted and sonicated to 500 bp. EBF1 (sc-137065, Santa Cruz Biotechnology; H00001879-M01, Abnova) and EZH2 (#5246, Cell Signaling) antibodies were used for chromatin immunoprecipitation (ChIP). Input DNA from cells prior to immunoprecipitation were used to normalize ChIP-seq peak calling. ChIPed DNA (10 ng) was used for ChIP with DNA sequencing (ChIP-seq) library construction following manufacturer protocols (New England Biolabs).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
37334678
Reads aligned (%)
98.5
Duplicates removed (%)
6.5
Number of peaks
1833 (qval < 1E-05)

hg19

Number of total reads
37334678
Reads aligned (%)
97.9
Duplicates removed (%)
7.8
Number of peaks
1529 (qval < 1E-05)

Base call quality data from DBCLS SRA