Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Cardiovascular
Cell type
Aortic valve interstitial cells
NA
NA

Attributes by original data submitter

Sample

source_name
Human aortic valve interstitial cells from non-mineralized aortic valves
cell type
aortic valve interstitial cells
antibody
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Human aortic valve interstitial cells were isolated from control non-mineralized aortic valves obtained from patients undergoing heart transplantation. The protocol was approved by the local ethical committee and informed consent was obtained from the subjects. Aortic leaflets were cut into pieces and incubated in 0.3% type I collagenase (Invitrogen, Thermo Fisher Scientific, ON, Canada) at 37°C for 45 minutes, then filtered through a 70 µm mesh, centrifuged for 5 minutes at 1,500 rpm and resuspended in complete media (DMEM, 10% FBS with L-glutamine and sodium pyruvate). Cells were used between passages 3 to 7. Nuclear extracts from VICs were immunoprecipitated with antibodies against H3K4me3, H3K4me1 (Cell Signaling Technology, New England Biolabs, ON, Canada) or H3K27Ac (Abcam, ON, Canada) pre-bound to protein G Dynabeads (Life Technologies, Thermo Fisher Scientific, ON, Canada). DNA was purified using DNA clean up & concentrator kit (Zymo Research, Cedarlane, Canada). Libraries were constructed using the QIAseq Ultralow Input Library Kit (Qiagen, ON, Canada) according to manufacturer's instructions. Sequencing was performed on an Illumina HiSeq4000 (UCSD IGM Genomics Facility, CA, USA).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
22422223
Reads aligned (%)
98.1
Duplicates removed (%)
14.6
Number of peaks
790 (qval < 1E-05)

hg19

Number of total reads
22422223
Reads aligned (%)
96.9
Duplicates removed (%)
15.9
Number of peaks
729 (qval < 1E-05)

Base call quality data from DBCLS SRA