Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3

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
cell line
HCT116
genotype
wildtype
antibody
rabbit anti H3 Cter (Zhang et al EMBO J, 24: 2379, 2005)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cross-linked Chromatin was sonicated with a Bioruptor 1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
8201096
Reads aligned (%)
96.5
Duplicates removed (%)
13.1
Number of peaks
97 (qval < 1E-05)

hg19

Number of total reads
8201096
Reads aligned (%)
96.2
Duplicates removed (%)
13.5
Number of peaks
103 (qval < 1E-05)

Base call quality data from DBCLS SRA