Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Blood
Cell type
L-1236
Primary Tissue
Blood
Tissue Diagnosis
Hodgkin's Lymphoma

Attributes by original data submitter

Sample

source_name
Hodgkin Lymphoma Cell Line
cell line
L1236
dsmz no
ACC 530
chip antibody
NFkB p65 (C-20) #sc-372, rabbit pkAb

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% Formaldehyde, lysed with 50 mM Tris-HCl, pH 8, 5mM EDTA, 1% SDS, sonicated with the Bioruptor (12 cycles), Setting M, 30 sec sonication/30 sec break per cycle. Immunoprecipitation and DNA-purification was performed according to the Upstate protocol. Libraries were prepared using Illumina's ChIP-Seq Sample Prep Kit (#IP-102-1001) according to the instructions of the manufacturer. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, size selection of the library was performed by excision of the region from 175 to 225 bp. DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Each library was validated using an Agilent 2100 bioanalyzer and sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
33640528
Reads aligned (%)
63.6
Duplicates removed (%)
12.2
Number of peaks
1170 (qval < 1E-05)

hg38

Number of total reads
45187468
Reads aligned (%)
55.4
Duplicates removed (%)
11.4
Number of peaks
1444 (qval < 1E-05)

Base call quality data from DBCLS SRA