Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RBPJ

Cell type

Cell type Class
Blood
Cell type
Mino
Tissue
Peripheral Blood/Mantle Cell Lymphoma (B Cell Non-Hodgkin's Lymphoma)
Cell Type
Lymphoblast
Disease
Mantle Cell Lymphoma

Attributes by original data submitter

Sample

source_name
Mino cell line
cell line
Mino
cell type
Mantle cell lymphoma cell line
drug treatment
DMSO
other treatment
Notch ligand (DLL1-IgG)
chip antibody
RBPJ (Cell Signaling, catalog #5313)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq: Cells were crosslinked by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a Branson sonifier in a 1% SDS-containing lysis buffer. Samples were diluted 1:10 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples, 1:10 diluted sonicated chromatin (whole cell extract; wce) was added directly to the reverse crosslinking step without immunoprecipitation. ChIP-Seq: Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced (38 bp x 2) on Illumina NextSeq.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
37713359
Reads aligned (%)
182.9
Duplicates removed (%)
2.8
Number of peaks
725 (qval < 1E-05)

hg38

Number of total reads
37713359
Reads aligned (%)
184.9
Duplicates removed (%)
2.6
Number of peaks
743 (qval < 1E-05)

Base call quality data from DBCLS SRA