Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
Monocytes-CD14+
Tissue
monocytes
Lineage
mesoderm
Description
Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis

Attributes by original data submitter

Sample

source_name
umbilical cord blood
tissue
umbilical cord blood
cell type
CD14+ monocytes
isolation
Miltenyi Biotec CD14+ magnetic bead isolation
age
under 30 weeks gestation preterm neonate
chip antibody
H3K4me3 (Abcam, ab8580, lot GR188707-1)

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 Genome Analyzer following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
57276495
Reads aligned (%)
2.0
Duplicates removed (%)
40.6
Number of peaks
381 (qval < 1E-05)

hg19

Number of total reads
57276495
Reads aligned (%)
2.0
Duplicates removed (%)
41.8
Number of peaks
359 (qval < 1E-05)

Base call quality data from DBCLS SRA