Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RAD21

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
ab992, Abcam

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

hg19

Number of total reads
19747406
Reads aligned (%)
62.4
Duplicates removed (%)
36.1
Number of peaks
21576 (qval < 1E-05)

hg38

Number of total reads
19747406
Reads aligned (%)
64.3
Duplicates removed (%)
34.7
Number of peaks
21698 (qval < 1E-05)

Base call quality data from DBCLS SRA