Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
POU2F2

Cell type

Cell type Class
Blood
Cell type
HBL-1
Primary Tissue
Blood
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Lymphoma

Attributes by original data submitter

Sample

source_name
HBL1 OCT2
cell line
HBL1
cell type
ABC DLBCL cells
disease state
activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
OCT2 (SC233) Antibody Extraction Other: 2.5 x 10(7) 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 x 10(7) chromatin cell equivalents were incubated overnight with 10 ug of OCT2 (SC233). The following day, chromatin/antibody complexes were incubated with 50 uL of protein G magnetic beads (Invitrogen) for 4 h at 4 C. 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
34713066
Reads aligned (%)
86.2
Duplicates removed (%)
10.9
Number of peaks
1933 (qval < 1E-05)

hg38

Number of total reads
34713066
Reads aligned (%)
87.7
Duplicates removed (%)
9.9
Number of peaks
1912 (qval < 1E-05)

Base call quality data from DBCLS SRA