Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
POU2F2

Cell type

Cell type Class
Blood
Cell type
BJAB
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
BJAB BirA OCT2 WT
cell line
BJAB
cell type
GCB DLBCL cells
disease state
germinal center B cell (GCB) subtype of diffuse large B cell lymphoma (DLBCL)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Streptavidin DynaBeads Other: Exponentially growing cells were cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 mins at RT and cells were washed twice with ice-cold PBS.  Cells were lysed in ice-cold RIPA buffer (10 mM Tris HCl, pH 8, 140 mM NaCl, 1 mM EDTA, pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.3% SDS, and 0.1% sodium deoxycholate) and DNA was sheared with a Misonix XL sonicator to an average fragment size of 300 nt.  For each immunoprecipitation reaction, 2.5 × 10(7) chromatin cell equivalents were incubated overnight with 50 ul of Streptavidin Dynal Beads (Invitrogen). Beads were washed four times with RIPA buffer, once with LiCl buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxy- cholate, 1 mM EDTA), once with TE, pH 8.0, and finally re-suspended in 100 uL of TE, pH 8, containing RNase A (0.2 ug/uL). Reverse cross-linking was performed overnight at 65 C, followed by treatment with 20 ug of proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIA- quick PCR purification columns (Qiagen). ChIP DNA was used to generate ChIP-Seq libraries using the TruSeq ChIP library preparation kit from Illumina according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
39201416
Reads aligned (%)
80.1
Duplicates removed (%)
14.4
Number of peaks
1982 (qval < 1E-05)

hg38

Number of total reads
39201416
Reads aligned (%)
81.7
Duplicates removed (%)
13.3
Number of peaks
3142 (qval < 1E-05)

Base call quality data from DBCLS SRA