Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Blood
Cell type
GM18507
Tissue
blood
Lineage
mesoderm
Description
lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed

Attributes by original data submitter

Sample

source_name
lymphoblastoid cell line
biomaterial_provider
GM18507
cell line
GM18507
cell type
lymphoblastoid cell line
population
YRI
ethnicity
Yoruba
country of origin
Nigeria
chip antibody
H3K4me1 (Millipore 07-436)
chip antibody manufacturer
Millipore

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
82589169
Reads aligned (%)
98.3
Duplicates removed (%)
48.2
Number of peaks
1022 (qval < 1E-05)

hg19

Number of total reads
82589169
Reads aligned (%)
97.4
Duplicates removed (%)
49.5
Number of peaks
1367 (qval < 1E-05)

Base call quality data from DBCLS SRA