Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
O30_H3K4me3_umbilical cord blood
age
30-36 weeks gestation preterm healthy neonate
tissue
umbilical cord blood
cell type
naive CD4+ T cells
isolation
Miltenyi Biotec naive CD4+ T cell magnetic bead isolation

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. DNA was end-repaired using a combination of T4 polynucleotide kinase and T4 DNA polymerase. The blunt phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a single 3' A to blunt DNA for ligation of Illumina adapters with a single 3' T overhang. After adapter ligation DNA was PCR amplified with Illumina adapters for 19 cycles and library fragments of ~250 bp (insert plus adapter and PCR primer) were selected by bead purification. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq 2500 following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
51075198
Reads aligned (%)
53.1
Duplicates removed (%)
9.5
Number of peaks
1352 (qval < 1E-05)

hg19

Number of total reads
51075198
Reads aligned (%)
52.6
Duplicates removed (%)
11.6
Number of peaks
1258 (qval < 1E-05)

Base call quality data from DBCLS SRA