Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TCF21

Cell type

Cell type Class
Cardiovascular
Cell type
HCASMC
NA
NA

Attributes by original data submitter

Sample

source_name
human coronary artery
cell type
primary human coronary artery smooth muscle cell (HCASMC) line
passage
passages 4-8
chip antibody
anti-Tcf21 antibody (Sigma #HPA013189)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross linked in 1% formaldehyde for 10 min and then washed with PBS. Cell pellets were frozen at -80C. All cell pellets were thawed on ice, combined for a total of 19.5 million cross linked cells and resuspended in cold PBS. PBS was removed and replaced with hypotonic buffer (20mM Hepes pH 7.9, 10mM KCl, 1mM EDTA, pH 8, 10% glycerol) and cells incubated on ice for 6 min. Cells were dounce homogenized with 20 strokes on ice using a 7ml glass homogenizer. Nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 4, constant duty for 12 rounds of 20 second pulses), resulting in chromatin fragments of 250-400 bp. Lysate was treated overnight at 4C with 5ug of anti-Tcf21 antibody (Sigma #HPA013189). Protein-DNA complexes were captured on Protein G agarose beads (Millipore Sigma #16-266) and eluted in 1% SDS TE buffer at 65C. After reverse cross linking, RNase A and proteinase K digestion, chromatin was purified using Qiagen PCR purification kit (Catalog #28106) sequencing libraries were generated according to Illumina DNA Sample Kit Instructions (Illumina Part # 0801– 0303, San Diego, CA)

Sequencing Platform

instrument_model
Illumina HiSeq X Ten

hg19

Number of total reads
515297944
Reads aligned (%)
24.2
Duplicates removed (%)
87.3
Number of peaks
44952 (qval < 1E-05)

hg38

Number of total reads
515297944
Reads aligned (%)
25.8
Duplicates removed (%)
86.6
Number of peaks
49668 (qval < 1E-05)

Base call quality data from DBCLS SRA