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
HCASMC Lonza 0000200212
cell type
coronary artery smooth muscle
chip antibody
TCF21
chip antibody manufacturer and catalog number
Abcam #ab49475, Lot No. 153899

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 Genome Analyzer II

hg19

Number of total reads
18000849
Reads aligned (%)
86.3
Duplicates removed (%)
5.9
Number of peaks
2629 (qval < 1E-05)

hg38

Number of total reads
18000849
Reads aligned (%)
88.0
Duplicates removed (%)
4.9
Number of peaks
2500 (qval < 1E-05)

Base call quality data from DBCLS SRA