Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
IRF4

Cell type

Cell type Class
Blood
Cell type
OCI-LY-3
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
ABC DLBCL
cell line
OCI-LY3
cell type
Diffuse large B-cell lymphoma (DLBCL)
chip antibody
sc-28696X, Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell fixation and chromatin sonication were optimised for each cell line in order to obtain enrichment of DNA fragments between 200-500bp. Chromatin was pre-cleared with BSA saturated Protein A sepharose (Thermo Scientific). A fraction of the chromatin was then incubated overnight at 4°C with the appropriate antibody (in duplicate) and then immunoprecipitated with BSA saturated Protein A sepharose (Thermo Scientific) for 4 hours at 4°C. Following washing to remove aspecificity, each IP was eluted from the Protein A sepharose overnight. DNA was then purified with standard phenol/chloroform extraction and quantified using Quant-iT™ Picogreen® dsDNA Broad-Range Assay Kit (Life Technologies™). IRF4, PU.1 and SPIB CHIP-seq libraries from OCI-LY3, OCI-LY10 and H929 were generated using the Illumina ChIP-seq Sample Prep Kit (Illumina®) according to manufacturer’s instructions. The BATF and the SPIB knockdown libraries were generated using the Microplex Library Preparation™ Kit (Diagenode) following manufacturer's instructions, and size selected using Agencourt® AMPure® XP beads (Beckman Coulter®).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
30974096
Reads aligned (%)
82.0
Duplicates removed (%)
16.4
Number of peaks
2219 (qval < 1E-05)

hg38

Number of total reads
30974096
Reads aligned (%)
83.1
Duplicates removed (%)
15.7
Number of peaks
2040 (qval < 1E-05)

Base call quality data from DBCLS SRA