Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Cardiovascular
Cell type
Fetal heart
NA
NA

Attributes by original data submitter

Sample

source_name
fetal heart, input ChIP
tissue
heart
developmental stage
PCW10
disease
-
antibody
-

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation were performed as previously described (PMID: 19212405) with some modifications. Briefly, frozen left ventricle tissue was pulverized with a mortar and pestle, resuspeneded in PBS, and cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp. Chromatin was inclubated for 2h at 4 C with 5 µg of antibody. Protein A and G Dynabeads (Invitrogen) were then added to this chromatin/antibody mixture for 30 minutes at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 37 C for one hour. Samples were treated with Proteinase K at 37 C and reverse-crosslinked overnight. Finally, the DNA was purified on Zymo ChIP clean and concentrate columns (Zymo Research) and the quality was assessed on the Agilent bioanalyzer. The ChIP-seq libraries were prepared using the Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2500 or 4000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
30479921
Reads aligned (%)
99.0
Duplicates removed (%)
2.2
Number of peaks
1230 (qval < 1E-05)

hg19

Number of total reads
30479921
Reads aligned (%)
97.8
Duplicates removed (%)
3.7
Number of peaks
1250 (qval < 1E-05)

Base call quality data from DBCLS SRA