Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EP300

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Colon cancer cell line
cell line
HCT116
cell type
human colon cancer cell
chip antibody
Santa Cruz (cat. no. SC-585)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP assays were performed as previously described (Lee et al., 2006) . Briefly, 5x10^7 cells were crosslinked with 1% paraformaldehyde (Electron microscropy science #15710) at room temperature for 10 min and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody. ChIP libraries were prepared with the TruSeq DNA Sample Kit (Illumina #FC-121-2001) according to Illumina's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
22999921
Reads aligned (%)
57.1
Duplicates removed (%)
37.8
Number of peaks
8006 (qval < 1E-05)

hg38

Number of total reads
22999921
Reads aligned (%)
58.6
Duplicates removed (%)
36.5
Number of peaks
7984 (qval < 1E-05)

Base call quality data from DBCLS SRA