Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Brd4

Cell type

Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
In vitro Th9_Ctrl
strain
C57BL/6
tissue
CD4+ T cell
chip antibody
BRD4

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed by using ChIP-IT® PBMC kit (#53042, Active Motif). Briefly, targeted T cells were harvested and fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Cells were resuspended in swelling buffer with detergent for 30 mins and centrifuged for 10 mins at 3200 g at 4 0C. Cell pellets were resuspended in 500ul ChIP buffer for chromatin sonication. Genomic DNA was sonicated to an average length of 300-500 bp. An aliquot of chromatin (25-30 ug) was pre-cleaned with protein A agarose beads. Epigenetically modified or transcription factor binding genomic DNA was isolated using specific antibody (4 μg). The following antibodies against mouse antigens were used: anti-Drd4 (A301-985A50, Bethyl Laboratiories); anti-H3K27Ac (#39133, Active Motif). DNA and protein complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 0C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps for end-polishing, dA-addition and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
37925636
Reads aligned (%)
97.4
Duplicates removed (%)
14.6
Number of peaks
9637 (qval < 1E-05)

mm9

Number of total reads
37925636
Reads aligned (%)
97.2
Duplicates removed (%)
14.6
Number of peaks
9631 (qval < 1E-05)

Base call quality data from DBCLS SRA