Antigen

Antigen Class

TFs and others

Antigen

SMARCA4

Cell type

Cell type Class

Blood

Cell type

CTV-1

Primary Tissue

Blood

Tissue Diagnosis

Leukemia

Sample

source_name

CTV-1_PU.1-delAmRNA_FA_BRG1-ChIP

cell line

CTV-1

cell type

T cell leukemia cell line

chip antibody

BRG1 (Abcam, #ab110641)

transfected ivt mrna

PU.1_delA

fixation method

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

hg38

Number of total reads

52499339

Reads aligned (%)

93.1

Duplicates removed (%)

14.5

Number of peaks

31264 (qval < 1E-05)

hg19

Number of total reads

52499339

Reads aligned (%)

92.4

Duplicates removed (%)

15.8

Number of peaks

31549 (qval < 1E-05)