Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NOTCH1

Cell type

Cell type Class
Blood
Cell type
REC-1
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
Rec-1 cell line
cell line
Rec-1
cell type
Mantle cell lymphoma cell line
drug treatment
GSI-washout
chip antibody
NICD1 (Cell Signaling, catalog #4147)

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
23854866
Reads aligned (%)
60.8
Duplicates removed (%)
68.5
Number of peaks
658 (qval < 1E-05)

hg38

Number of total reads
23854866
Reads aligned (%)
63.3
Duplicates removed (%)
67.6
Number of peaks
682 (qval < 1E-05)

Base call quality data from DBCLS SRA