Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

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
Lymphoblast Cell Line
cell type
EBV-infected B Lymphocytes
cell line
GM12878
chip antibody
Bethyl Labs A301-985A lot A301-985A-1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde. After wash with PBS, the cells were lyzed in ChIP lysis buffer. Lysates were sonicated and cleared by centrifugation. After pre-clear with protein A beads, antibody (Bethyl Labs A301-985A lot A301-985A-1) was incubated with the lysate overnight at 4°C. Protein A was used to capture the protein DNA complex. The eluted protein DNA complexes were reverse crosslinked and DNA was purified by a Qiagen PCR purification column. Libraries were prepared using ChIP-Seq Library Prep Reagent Set for Illumina from NEB. Briefly, DNA was end-repaired. 3' A base was added and ligated to adaptors. After PCR amplification, DNA was purified and analyzed with Illumina HiSeq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
32179447
Reads aligned (%)
85.4
Duplicates removed (%)
10.7
Number of peaks
997 (qval < 1E-05)

hg38

Number of total reads
32179447
Reads aligned (%)
87.2
Duplicates removed (%)
9.7
Number of peaks
1131 (qval < 1E-05)

Base call quality data from DBCLS SRA