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
human aortic endothelial cell
cell type
HAEC
passage
6 to 10
chip antibody
H3K27ac, Active Motif #39135
treatment
control, 4h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, Cells were fixed with formaldehyde, lysates were sonicated, and complexes precipitated with antibody. For RNA-seq, RNA was extracted using the the Quick-RNA Micro Prep kit from ZymoResearch and poly-A selected. For ATAC-seq, nuclei were extracted with nuclear isolation buffer and DNA was size-selected for 125-175 bp fragments on a TBE gel For RNA-seq, cDNA was synthesized using the SuperScript III system from Invitrogen, followed by second strand synthesis, ds End Repair and UDG treatment to recover strand-specific libraries. Libraries were barcoded with BioO Nextflex adapters and amplified prior to sequencing. ChIP-seq libraries were synthesized similarly omiting the UDG treatment. ATAC-seq libraries were extracted from TBE gel, amplified, and sequenced.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
29916605
Reads aligned (%)
98.9
Duplicates removed (%)
59.2
Number of peaks
31852 (qval < 1E-05)

hg19

Number of total reads
29916605
Reads aligned (%)
98.5
Duplicates removed (%)
59.7
Number of peaks
31779 (qval < 1E-05)

Base call quality data from DBCLS SRA