Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
IRF4

Cell type

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

Attributes by original data submitter

Sample

source_name
Blood
cell type
CD4 T cells
chip antibodies
IRF4 (Santa Cruz Biotechnology; sc-6059X; M-17; polyclonal)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP assays were performed with activated B cells by fixing for 10 min at 25 °C with 11% formaldehyde followed by chromatin isolation and shearing by sonication for 7 min (10% duty cycle, 175 pulses and 200 bursts; Covaris). 5 or 10 μg chromatin was subjected to immunoprecipitation with a-H3K27Ac (1 μg; Diagenode), a- NFATc1 (1 μg, 7A6; Santa Cruz Biotechnology), a-NFATc2 (1 μg, 4G6-G5; Santa Cruz Biotechnology), a-IRF4 (1 μg, M-17; Santa Cruz Biotechnology) or a-IRF8 (2 μg, C-19; Santa Cruz Biotechnology). After washing, elution, and reversal of cross-links, DNA was isolated by phenol/chloroform extraction and used in PCR reactions that were performed with the primers provided in the Extended Data For ChIP-seq analyses, activated B cells (24 h) were transduced with retroviral vectors as described above. Cells (48 h after transduction) were crosslinked with formaldehyde as described above and chromatin was subjected to immunoprecipitation with a-HA (1 μg, 12CA5; Roche). For ChIP-seq analysis with hCD4 T cells a-CD3 and a-CD28 beads were used for activation. Cross-linked chromatin was immunoprecipitated with a-NFATc1, a-NFATc2 (1 μg, 25A10.D6.D2, ThermoFIscher Scientific) or a-IRF4 using IP-STAR robot (Diagenode). DNA libraries were prepared with a ThruPLEX-FD Prep Kit (Rubicon Genomics) or using chipmentation aproach. The amplified products were purified with AMPure XP beads (Beckman Coulter) and subjected to single or paired end-sequencing on an Illumina HiSeq2500 machine. Each sample was used to generate ~1 X 10^7 reads. RNA-seq libraries were generated from 300 ng total RNA with an RNA Sample Prep Kit (Illumina) according to the manufacturer's protocol. The libraries were subjected to paired-end sequencingat CCHMC DNA sequencing core using . Each sample was used to generate ~2 X 10^7 reads. RNA libraries for single read sequencing were prepared by using standard Illumina protocols. ChIP libraries were prepared by using ThruPLEX DNA kit (Rubicon) or by chipmentation.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
11128426
Reads aligned (%)
79.3
Duplicates removed (%)
7.0
Number of peaks
6989 (qval < 1E-05)

hg38

Number of total reads
11128426
Reads aligned (%)
80.7
Duplicates removed (%)
6.0
Number of peaks
7193 (qval < 1E-05)

Base call quality data from DBCLS SRA