Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Th2 Cells
MeSH Description
A subset of helper-inducer T-lymphocytes which synthesize and secrete the INTERLEUKINS IL-4; IL-5; IL-6; and IL-10. These cytokines influence B-cell development and antibody production as well as augmenting humoral responses.

Attributes by original data submitter

Sample

source_name
cultured TH2 cells
cell type
cultured TH2 cells
genotype
Batf1/3DKO
stimulation
secondary stimulation
chip antibody
no antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 8 min at room temperature, quenched with 1.25M Glycine, twice washed with PBS. Chromatin was sonicated for shearing DNA size from 140 to 300 bp. Chromatin fragments were immunoprecipitated overnight at 4 °C with Dynabeads Protein A or G bound to anti-BATF or anti-IRF-4 (sc-6059x, Santa Cruz Biotechnology). For ChIP-seq, ChIPed DNA was eluted and reverse-crosslinked for 6 hr. DNA was purified with phenol:chloroform extraction followed by ethanol precipitation. For ChIP-exo, see library construction protocol. For ChIP-seq, libraries were prepared using ThruPLEX-FD kit (Rubicon Genomics). For ChIP-exo, ChIPed DNA were performed by the following enzymatic reactions; End polishing, ligation of P7 exo-adaptor, nick repair, exonuclease reaction. DNA was eluted and reverse crosslinked. The libraries were generated by P7 primer extension, ligation of P5 exo-adaptor, PCR amplification for 12 cycles and were cleaned up by AMPure XP. All libraries were sequenced using Illumina HiSeq 2500 as single reads extending 50 bases.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
47067376
Reads aligned (%)
98.0
Duplicates removed (%)
13.0
Number of peaks
526 (qval < 1E-05)

mm9

Number of total reads
47067376
Reads aligned (%)
97.7
Duplicates removed (%)
13.0
Number of peaks
576 (qval < 1E-05)

Base call quality data from DBCLS SRA