Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BCL6

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
SUDHL4 cells (lymphoma)
cell line
SUDHL4
cell type
lymphoma cell line
chip antibody
BCL6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, SUDHL4 were fixed, lysed, and sonicated to generate fragments less than 400 bp. Sonicated lysates were incubated with antibodies against LSD1 (abcam 17721), BCL6 (Santa Cruz N3, sc-858), or H3K4me1 (abcam, ab8895), and after increasing stringency washes, immunocomplexes were recovered and DNA was isolated. H3K4me1 ChIPs also contained Drosophila spike-in chromatin control (750ng per ChIP, Active Motif, 53083) added during precipitation along with Drosophila antibody (2ug, Active Motif, 61686) per manufacturer's recommendation for proper signal normalization. ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacturer's instructions with minor modifications. Briefly, 10ng of purified ChIP DNA (quantified using Qubit 2.0 fluorometer, Invitrogen) was end repaired by conversion of overhangs to phosphorylated blunt ends. A' bases were added to the 30 ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adaptor ligation, DNA was separated by electrophoresis and size selected by isolating a gel band of 250 ± 25bp. Size selected fragments were PCR amplified for 15 cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30 s at 98oC, 15cycles of 10 at 98oC, 30 s at 65oC, 30 s at 72oC and 5min extension at 75oC). Q-PCR was repeated to confirm retention of relative enrichment.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
66591384
Reads aligned (%)
84.9
Duplicates removed (%)
8.7
Number of peaks
37282 (qval < 1E-05)

hg38

Number of total reads
66591384
Reads aligned (%)
86.8
Duplicates removed (%)
7.3
Number of peaks
37089 (qval < 1E-05)

Base call quality data from DBCLS SRA