Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RAD21

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
Rad21-ChIP-seq-HCT_DAU
cell line
HCT116
cell type
Colon carcinoma cells
growth phase
exponential growth phase
treated with
250 nM daunorubicin for 8hrs
chip antibody
Rad21 (AbCam 992)

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

hg19

Number of total reads
26770715
Reads aligned (%)
185.4
Duplicates removed (%)
3.1
Number of peaks
37672 (qval < 1E-05)

hg38

Number of total reads
26770715
Reads aligned (%)
186.1
Duplicates removed (%)
3.1
Number of peaks
37788 (qval < 1E-05)

Base call quality data from DBCLS SRA