Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Irf4

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
ChIP-seq IRF4 Act B cell
strain background
C57BL/6
genotype/background
Wild-type
cell preparation
2-day LPS stimulation, MACS sorted
cell type
Act B cell
cell sorting strategy
n.a.
chip antibody
Irf4 Ab, SantaCruz SC6059X, lot: E0608

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
phenol-chloroform extraction About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext Ultra End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer’s guidelines.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
33849471
Reads aligned (%)
94.5
Duplicates removed (%)
15.0
Number of peaks
9437 (qval < 1E-05)

mm9

Number of total reads
33849471
Reads aligned (%)
94.2
Duplicates removed (%)
15.0
Number of peaks
9447 (qval < 1E-05)

Base call quality data from DBCLS SRA