Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TBX21

Cell type

Cell type Class
Blood
Cell type
Th1 Cells
MeSH Description
A subset of helper-inducer T-lymphocytes which synthesize and secrete INTERLEUKIN-2; INTERFERON-GAMMA; and INTERLEUKIN-12. Due to their ability to kill antigen-presenting cells and their lymphokine-mediated effector activity, Th1 cells are associated with vigorous delayed-type hypersensitivity reactions.

Attributes by original data submitter

Sample

source_name
In vitro differentiated Th1 cells
cell type
Th1
antibody
anti-T-bet SY4530FB
treatment/agent
anti-CD3/CD28

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen. Cells were lysed with non-ionic detergent, nuclei washed and then lysed with ionic detergent. Cells were sonicated on ice to solubilize and shear crosslinked DNA (24W for 10 x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell extract was cleared by centrifugation and then incubated overnight at 4°C with 100 µl of Dynal Protein G magnetic beads that had been pre-incubated with 20 µl of anti-T-bet serum. Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with occasional vortexing and crosslinks then reversed in IP and input DNA by overnight incubation at 65°C. IP and input DNA were then purified by treatment with RNase A, proteinase K and phenol:chloroform extraction followed by ethanol precipitation. Libraries were constructed from ChIP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit and Agilent bioanalyzer, pooled and subjected to 150 bp single-end read sequencing with an Illumina NextSeq sequencer.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
109794688
Reads aligned (%)
58.9
Duplicates removed (%)
27.8
Number of peaks
53481 (qval < 1E-05)

hg38

Number of total reads
109794688
Reads aligned (%)
60.2
Duplicates removed (%)
26.7
Number of peaks
53905 (qval < 1E-05)

Base call quality data from DBCLS SRA