Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

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

Attributes by original data submitter

Sample

source_name
Endothelial Cells
cell type
immortalized Human Aortic Endothelial Cells
passages
passages 23 to 25
chip antibody
H3K27ac (Diagenode; C15410196)
tnf-alpha treatment
4h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were washed with HBSS Gibco and fixed in paraformaldehyde (PFA) 1% for 10 minutes at room temperature (RT). PFA was quenched in 134 mM glycine for 5 minutes at RT. Fixed cells were washed with ice-cold PBS and collected with a cell scraper in ice-cold PBS. Cells were pelleted by centrifugation, washed in ice-cold PBS, and pelleted again before snap freezing in liquid nitrogen. Fixed cells were subject to lysis in 5 mM PIPES-pH 8.5, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate and protease inhibitor cocktail. Nuclei were then lysed in 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate and protease inhibitor cocktail. Chromatin immunoprecipitation was performed as previously described using 3.7 μg of H3K27ac antibody (Diagenode) per samples containing 1 to 1.5 million of cells (no antibody for input). Library construction was performed using KAPA Hyper Prep Kit (Kapa Biosystems) for Illumina using with adapters from TruSeq DNA LT Sample Prep Kit (Illumina)

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
107909998
Reads aligned (%)
97.0
Duplicates removed (%)
44.7
Number of peaks
46240 (qval < 1E-05)

hg19

Number of total reads
107909998
Reads aligned (%)
96.5
Duplicates removed (%)
45.0
Number of peaks
44813 (qval < 1E-05)

Base call quality data from DBCLS SRA