Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Blood
Cell type
BJAB
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
BJAB cell line
cell type
b cell lymphoma cell line
passages
2-5
cell line
BJAB
chip antibody
RelA (sc-372, Santa Cruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. For sequencing, adapters were ligated to the precipitated DNA fragments or the input DNA to construct a sequencing library according to the manufacturer's protocol (Illumina, San Diego, CA). Adapters with a T overhang were ligated to the DNA fragments and size selected (~200 - 350 bases) on a 4.5% agarose gel. 18-cycles PCR amplification were performed to enrich for fragments with an adaptor on both ends. These samples were bound to an Illumina single-read Flowcell, followed by cluster generation on the Illumina Cluster Station, and sequencing with Illumina Genome Analyzer (GA-II).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
21917642
Reads aligned (%)
92.2
Duplicates removed (%)
4.9
Number of peaks
2582 (qval < 1E-05)

hg38

Number of total reads
21917642
Reads aligned (%)
93.5
Duplicates removed (%)
4.2
Number of peaks
2488 (qval < 1E-05)

Base call quality data from DBCLS SRA