Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AICDA

Cell type

Cell type Class
Blood
Cell type
U-2932
Primary Tissue
Blood
Site of Extraction
Ascites
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
U-2932 (RRID:CVCL_1896)
chip antibody
anti-AID antibody (ab59361, Abcam; 1:2000 dilution)
cell type
Diffuse large B-cell lymphoma activated B-cell type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Exponentially growing cells were cross-linked with 1% formaldehyde and then quenched with glycine for 5 min at RT followed by lysis and MNase digestion. Samples were sonicated for 60 min using the Bioruptor (Diagenode) For each immunoprecipitation reaction, 4x106 chromatin cell equivalent were incubated overnight with either an AID antibody (Abcam, ab59361) or a rabbit IgG negative control antibody, subjected to protein A/G magnetic bead binding, IP elution and DNA recovery. The ChIP DNA was used to generate ChIPseq libraries with the ChIP-Seq sample preparation kit (Illumina) for sequencing at the Arkansas Children's Research Institute Genomics Core.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
76778039
Reads aligned (%)
187.8
Duplicates removed (%)
3.8
Number of peaks
1060 (qval < 1E-05)

hg38

Number of total reads
76778039
Reads aligned (%)
190.4
Duplicates removed (%)
3.5
Number of peaks
1869 (qval < 1E-05)

Base call quality data from DBCLS SRA