Antigen

Antigen Class

Histone

Antigen

H3K4me3

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

Sample

source_name

lymphoblastoid cells

biomaterial_provider

GM12878

cell line

GM12878

agent

doxorubicin

chip antibody

rabbit polyclonal anti-trimethyl-Histone H3 (Lys4) antibody (Millipore, cat# 07-473)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Lysates were clarified from sonicated nuclei and H3K4me3-DNA complexes were isolated with rabbit polyclonalanti-trimethyl-Histone H3 (Lys4) antibody (Millipore, cat# 07-473). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

Sequencing Platform

instrument_model

Illumina Genome Analyzer II

hg38

Number of total reads

36282232

Reads aligned (%)

92.9

Duplicates removed (%)

69.1

Number of peaks

23723 (qval < 1E-05)

hg19

Number of total reads

36282232

Reads aligned (%)

92.7

Duplicates removed (%)

69.3

Number of peaks

24388 (qval < 1E-05)