Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ING2

Cell type

Cell type Class
Digestive tract
Cell type
RKO
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
human colon carcinoma
ChIP
ING2
cell line
RKO
growth conditions
untreated cells, normal growth conditions
antibody vendor/catalog
epitomics, 3683-1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the Illumina Genome analyzer or HiSeq2000 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
224670611
Reads aligned (%)
60.7
Duplicates removed (%)
30.8
Number of peaks
54583 (qval < 1E-05)

hg38

Number of total reads
224670611
Reads aligned (%)
62.6
Duplicates removed (%)
29.2
Number of peaks
50937 (qval < 1E-05)

Base call quality data from DBCLS SRA