Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Blood
Cell type
CTV-1
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
CTV-1_mutPU.1mRNA_DSG_FA_BRG1-ChIP
cell line
CTV-1
cell type
T cell leukemia cell line
chip antibody
BRG1 (Abcam, #ab110641)
transfected ivt mrna
PU.1mut
fixation method
DSG_FA
preperation batch
4

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were preparated from sonicated nuclei and protein/histone-DNA complexes were isolated with antibody. ChIP construction was essentially done as described (Pham et al. 2012) with slight modifications for BRG1, ETS1 and FLI1 samples, which were prepared using dual crosslinking with 2 mM DSG (Thermo Fisher Scientific) and 1% formaldehyde. Libraries for sequencing were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 550

hg19

Number of total reads
46706026
Reads aligned (%)
72.6
Duplicates removed (%)
20.2
Number of peaks
24400 (qval < 1E-05)

hg38

Number of total reads
46706026
Reads aligned (%)
74.4
Duplicates removed (%)
18.9
Number of peaks
24091 (qval < 1E-05)

Base call quality data from DBCLS SRA