Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
GM12878
biomaterial_provider
CC
cell line
GM12878

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Exponentially growing cells from ENCODE Tier 1 and Tier 2 cell lines were crosslinked in 1% formaldehyde and harvested in batches of 20 million cells per replicate.  Prepared nuclei were resuspended in RIPA buffer and chromatin shearing was performed on a Bioruptor Twin instrument (Diagenode). Antibody (5 µg/rxn) was coupled to M-280 Dynabeads (ThermoFisher Scientific; 11201) overnight prior to addition of sheared chromatin. A small aliquot of the sheared chromatin was reserved as an input control. Following incubation and wash steps, captured chromatin and input control were reverse crosslinked overnight at 65°C and recovered using the QIAquick PCR Purification System (Qiagen; 28104). ChIP-seq libraries (illumina) were prepared and run on an Illumina HiSeq 2500 instrument.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
25985259
Reads aligned (%)
75.2
Duplicates removed (%)
7.2
Number of peaks
5893 (qval < 1E-05)

hg19

Number of total reads
25985259
Reads aligned (%)
74.3
Duplicates removed (%)
8.1
Number of peaks
6167 (qval < 1E-05)

Base call quality data from DBCLS SRA