Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
Lymphoblastoid cell lines
biomaterial_provider
CC
cell line
GM12878
antibody
Santa Cruz Biotechnology #sc-372

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
GM12878 cells were cross-linked with 1% formaldehyde. Chromatin was sonicated to an average size of 500 bp. Biological replicates were obtained using cells grown on separate days. Antibodies against RelA, RelB, cRel, p50 and p52 were used to immunoprecipitate protein-DNA complexes. Captured protein-DNA complexes were eluted from protein A beads and reverse-crosslinked. Eluted DNA was purified using PCR purification columns (Qiagen). ChIP-seq libraries were prepared using NEBNext library preparation kits (New England Biolabs)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
150187141
Reads aligned (%)
47.2
Duplicates removed (%)
49.4
Number of peaks
18204 (qval < 1E-05)

hg38

Number of total reads
150187141
Reads aligned (%)
48.5
Duplicates removed (%)
48.4
Number of peaks
17635 (qval < 1E-05)

Base call quality data from DBCLS SRA