Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Blood
Cell type
Lymphoblastoid cell line
Tissue
blood
Lineage
mesoderm
Description
parental cell type to lymphoblastoid cell lines

Attributes by original data submitter

Sample

source_name
Lymphoblastoid Cell Line
cell line
GM19144
antibody
H3K4ME1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C. ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
26962207
Reads aligned (%)
99.3
Duplicates removed (%)
14.9
Number of peaks
48387 (qval < 1E-05)

hg19

Number of total reads
26962207
Reads aligned (%)
98.8
Duplicates removed (%)
14.9
Number of peaks
49172 (qval < 1E-05)

Base call quality data from DBCLS SRA