Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BANP

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
HCT116 p53+/+ cell line
cell line
HCT116
cell type
Human colorectal carcinoma
chip antibody
SMAR1/BANP (Bethyl Laboratories, A300-279A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed using ChIP assay kit (Upstate Biotechnology) following the manufacturer’s instructions. Lysates obtained after sonication were subjected to pull down with antibody. ChIP enriched DNA was subjected to library construction using Illumina's "Preparing samples for ChIP sequencing of DNA" kit. Briefly, DNA ends were repaired and phosphorylated. 3'-dA overhangs were generated using Klenow (exo-) and dATP. Thereafter, the adaptors were ligated. PCR amplification for 18 cycles and size selection was performed.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
14285728
Reads aligned (%)
28.1
Duplicates removed (%)
6.3
Number of peaks
7964 (qval < 1E-05)

hg38

Number of total reads
14285728
Reads aligned (%)
28.3
Duplicates removed (%)
6.0
Number of peaks
7896 (qval < 1E-05)

Base call quality data from DBCLS SRA