Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Cdk9

Cell type

Cell type Class
Embryonic fibroblast
Cell type
NIH/3T3
Primary Tissue
Embryo
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
NIH3T3 fibroblasts
culture condition
serum starved and re-fed
chemicals
JQ1
chip antibody
CDK9 (Santa Cruz Biotechnology, sc-8338)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody. ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on HiSeq 2000 or 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
50844311
Reads aligned (%)
96.6
Duplicates removed (%)
73.4
Number of peaks
1003 (qval < 1E-05)

mm9

Number of total reads
50844311
Reads aligned (%)
96.4
Duplicates removed (%)
73.5
Number of peaks
1023 (qval < 1E-05)

Base call quality data from DBCLS SRA