Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3ac

Cell type

Cell type Class
Cardiovascular
Cell type
HAEC
Primary Tissue
Aorta
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HAEC H3K9/14ac control
cell type
Primary Human Aortic Endothelial Cells (HAECs)
passages
Passage 4-6
chip antibody
Anti-acetyl-Histone H3
chip antibody vendor
Millipore

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After the incubation,HAECs were fixed for 10 minutes with 1% formaldehyde. Glycine (0.125 M) solution was then added for another 10 minutes. Cell pellets were resuspended in SDS lysis buffer containing protease inhibitors. Then cells were sonicated to shear chromatin and ChIP was performed using indicated above antibodies and DynaMag™-2 magnet (Invitrogen). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. 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 (32 to 52 exo minus) 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 DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
26678620
Reads aligned (%)
99.2
Duplicates removed (%)
6.1
Number of peaks
23970 (qval < 1E-05)

hg19

Number of total reads
26678620
Reads aligned (%)
98.9
Duplicates removed (%)
6.4
Number of peaks
23905 (qval < 1E-05)

Base call quality data from DBCLS SRA