Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Cardiovascular
Cell type
HCASMC
NA
NA

Attributes by original data submitter

Sample

source_name
HCASMC Lonza 0000317155
cell type
coronary artery smooth muscle
chip antibody
IgG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Ten million HCASMC cells per condition were crosslinked for 10 min with 1% formaldehyde. Cells were lysed for 10 min on ice, and nuclei were then lysed for 10 min on ice. Crosslinked chromatin was sheared for 3x5 min by sonication using a Bioruptor and pre-cleared with 10 µg anti-rabbit IgG pre-immune serum. TCF21 ChIP was performed overnight in IP dilution buffer using anti-TCF21 (Sigma-Aldrich, St. Louis, MA, USA, #HPA013189, Lot. No. R02939 (Ab1) or Abcam, Cambridge, UK, #ab49475, Lot No. 153899 (Ab2)) or anti-rabbit IgG respectively. JUN and JUND ChIP was performed with Santa Cruz Biotechnology sc-1694 and Santa Cruz Biotechnology sc-74 respectively. After reverse-crosslinking, RNaseA and proteinase K digestion, chromatin was cleaned up using the Qiagen PCR purification kit

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
53615941
Reads aligned (%)
95.4
Duplicates removed (%)
17.4
Number of peaks
2288 (qval < 1E-05)

hg19

Number of total reads
53615941
Reads aligned (%)
94.2
Duplicates removed (%)
17.9
Number of peaks
946 (qval < 1E-05)

Base call quality data from DBCLS SRA