Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Blood

Cell type

GM19239

Tissue

blood

Lineage

mesoderm

Description

B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed

Sample

source_name

lymphoblastoid cell line

biomaterial_provider

GM19239

cell line

GM19239

cell type

lymphoblastoid cell line

population

YRI

ethnicity

Yoruba

country of origin

Nigeria

chip antibody

H3K4me3 (Abcam ab8580)

chip antibody manufacturer

Abcam

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples chromatin was sheared with a Covaris S2 (settings: 40 min duty cycle 20%, intensity 8, 200 cycles/burst, 500 uL at a time in 12 x 24 mm tubes). Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.

Sequencing Platform

instrument_model

Illumina Genome Analyzer IIx

hg38

Number of total reads

41049455

Reads aligned (%)

98.5

Duplicates removed (%)

19.1

Number of peaks

28099 (qval < 1E-05)

hg19

Number of total reads

41049455

Reads aligned (%)

97.5

Duplicates removed (%)

20.4

Number of peaks

29312 (qval < 1E-05)