Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
STAT3

Cell type

Cell type Class
Blood
Cell type
SU-DHL-4
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
B cells
disease state
diffuse large B cell lymphoma (DLBCL)
dlbcl subtype
GCB
cell line
SU-DHL4
chip antibody
STAT3 (Santa Cruz, sc-482X)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinked cell pellets were dounce homogenized to collect nuclei. Nuclear lysate was sonicated, then immunoprecipitated. Antibody-protein-DNA complexes were collected using Protein A agarose beads. Libraries were prepared according to Illumina's instructions using non-Illumina enzymes and kits. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase (End-It Repair Kit, Epicenter-Illumina). The blunt ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. DNA was then gel purified and size selected for 150-300 bp fragments to exclude unligated adapters, PCR amplified with Illumina primers using Phusion high-fidelity DNA polymerase for 15 cycles, and size selected again from an agarose gel for 150-300 bp fragments. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
154348871
Reads aligned (%)
70.3
Duplicates removed (%)
21.9
Number of peaks
21699 (qval < 1E-05)

hg38

Number of total reads
154348871
Reads aligned (%)
72.2
Duplicates removed (%)
20.5
Number of peaks
22473 (qval < 1E-05)

Base call quality data from DBCLS SRA