Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
Colorectal carcinoma cells
cell line
HCT116
cell type
Colorectal carcinoma
tissue
colon
culture
Collected in exponential growth phase
cell type
Epithelial

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP were performed as described in Gevry N, Chan HM, Laflamme L, Livingston DM, Gaudreau L. p21 transcription is regulated by differential localization of histone H2A.Z. Genes & development. 2007;21(15):1869-81. PubMed PMID: 17671089 except for the following steps. For each treatment conditions six immuno-precipitations were performed. Immuno-precipitations were performed using Dynabeads coupled to protein A (Life Technologies) without pre-clearing. The libraries for deep-sequencing were prepared from 10 ng ChIPed DNA using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
40200306
Reads aligned (%)
98.1
Duplicates removed (%)
3.1
Number of peaks
43213 (qval < 1E-05)

hg19

Number of total reads
40200306
Reads aligned (%)
97.7
Duplicates removed (%)
3.3
Number of peaks
42862 (qval < 1E-05)

Base call quality data from DBCLS SRA