Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EZH2

Cell type

Cell type Class
Blood
Cell type
Pfeiffer
Primary Tissue
Blood
Tissue Diagnosis
Hodgkin's Lymphoma

Attributes by original data submitter

Sample

source_name
Pfeiffer cell line
cell type
Pfeiffer cell line
treatment
NA
chip antibody
anti-EZH2 (Millipore, 07-689, lot DAM1834941)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as previously described (Ci et al., Blood, 2009). Briefly, 108 cells were fixed with 1% formaldehyde, lysed, and sonicated (Branson Sonicator; Branson) leading to a DNA average size of 200 bp. Five µg of antibodies were added to the precleared sample and incubated overnight at 4°C. The complexes were purified using protein-A beads (Roche) followed by elution from the beads and decrosslinking. DNA was purified using PCR purification columns (QIAGEN). ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
89947137
Reads aligned (%)
65.5
Duplicates removed (%)
26.0
Number of peaks
1688 (qval < 1E-05)

hg38

Number of total reads
89947137
Reads aligned (%)
67.2
Duplicates removed (%)
24.6
Number of peaks
1872 (qval < 1E-05)

Base call quality data from DBCLS SRA