Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
CD4+ T cells
strain
C57BL/6
genotype
WT
culture condition
ChIP-seq in vitro culture protocol (IFN-γ)
chip antibody
N/A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA Sequencing (RNA-seq) was performed and analyzed as described previously. Total RNA was prepared from approximately 1 million cells by using TRIzol or mirVana miRNA Isolation Kit (Thermo Fisher Scientific Inc.). 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol. RNA-seq: 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol. RNA-seq: The libraries were sequenced for 50 cycles (single read) with a HiSeq 2000 or HiSeq 2500 (Illumina) ChIP-seq: Cells cultured as indicated were cross-linked for 10 minutes with 1% formaldehyde and harvested. Cells were lysed by sonication and immunoprecipitated with anti-T-bet (sc-21003, Santa Cruz Biotechnology), anti- STAT1 (sc-592, Santa Cruz Biotechnology), anti-STAT2 (ab124283, AbCam), anti-H3K4m1 (ab8895, AbCam) and anti-H3K27ac (ab4729, AbCam) ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt-ended, then phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen). ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
37365575
Reads aligned (%)
98.9
Duplicates removed (%)
21.7
Number of peaks
2330 (qval < 1E-05)

mm9

Number of total reads
37365575
Reads aligned (%)
98.8
Duplicates removed (%)
21.7
Number of peaks
2208 (qval < 1E-05)

Base call quality data from DBCLS SRA