Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Blood
Cell type
RAJI
Primary Tissue
Blood
Tissue Diagnosis
Malignant Lymphoma - Burkitts Type

Attributes by original data submitter

Sample

source_name
Raji (lymphocyte)
cell type
Raji (EBNA 1 positive)
genotype/variation
Expressing amanitin-resistant R1810A mutant POLR2A
antibody
RNAPII (N20) (Santa Cruz pAb Cat # sc-899)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10e7-10e8 cells were cross-linked for 10 min in 1% formaldehyde. Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). RNAPII was immunoprecipitated with 2ug of antibodies and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic). Sequencing libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina) according the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
29770019
Reads aligned (%)
87.7
Duplicates removed (%)
25.3
Number of peaks
1225 (qval < 1E-05)

hg19

Number of total reads
29770019
Reads aligned (%)
86.7
Duplicates removed (%)
26.3
Number of peaks
1435 (qval < 1E-05)

Base call quality data from DBCLS SRA