Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me3

Cell type

Cell type Class
Cardiovascular
Cell type
HUVEC
Primary Tissue
Umbilical Cord
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
human umbilical vein endothelial cells
cell type
human umbilical vein endothelial cells (HUVEC)
antibody
39161, Active motif

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with NEXTflex DNA barcodes and library fragments were size-selected (230-350bp) from a 10% TBE-gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq 2000 according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
20109737
Reads aligned (%)
98.5
Duplicates removed (%)
4.0
Number of peaks
5145 (qval < 1E-05)

hg19

Number of total reads
20109737
Reads aligned (%)
97.6
Duplicates removed (%)
5.5
Number of peaks
5120 (qval < 1E-05)

Base call quality data from DBCLS SRA