Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SUZ12

Cell type

Cell type Class
Blood
Cell type
KARPAS-422
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma Non-Hodgkins

Attributes by original data submitter

Sample

source_name
Diffuse large B cell lymphoma
cell line
KARPAS-422
treatment
DMSO 8 days
chip antibody target
Suz12
chip antibody
Active Motif 39357

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were pelleted, fixed in 1% formaldehyde for 10 mins, lysed and sonicated. Chromatin samples were precleared with Protein A Dynabeads (Life Technologies), and incubated overnight at 40C with anti-EZH2 (Millipore 07-689), anti-H3K27me3 (Cell Signaling Techonology 9730), anti-SUZ12 (Active Motif 39357), and anti-H3K4me3 (Abcam ab8580). Chromatin-antibody complexes were precipitated using Protein A Dynabeads followed by washes in RIPA buffer and Tris/ EDTA. Samples were digested with RNAase A, treated with Proteinase K and 10% SDS, followed by cross-link reversal at 650C. DNA was purified using MinElute PCR purification kits (Qiagen). DNA libraries for ChIP-seq were prepared using Ovation Ultralow DR Multiplex System kits (0330-32, NuGEN) followed by Illumina sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
28468534
Reads aligned (%)
73.0
Duplicates removed (%)
11.3
Number of peaks
1124 (qval < 1E-05)

hg38

Number of total reads
28468534
Reads aligned (%)
74.6
Duplicates removed (%)
10.2
Number of peaks
1067 (qval < 1E-05)

Base call quality data from DBCLS SRA