Antigen

Antigen Class

DNase-seq

Antigen

DNase-Seq

Cell type

Cell type Class

Blood

Cell type

PBMC

Tissue

blood

Lineage

mesoderm

Description

peripheral blood mononuclear cells

Sample

source_name

PBMC

tissue

PBMC

dnase units

8

disease state

presentation ALL patient

Sequenced DNA Library

library_strategy

DNase-Hypersensitivity

library_source

GENOMIC

library_selection

DNase

library_construction_protocol

DNase I (Worthington) digestion was performed using ~5 million patient sample cells using 8 units (presentation) or 14 units (relapse) for 3 min at 22 °C in a 1 mM CaCl2 supplemented buffer. Nuclear proteins were digested with 1 mg/ml Proteinase K overnight at 37 °C. DNaseI digestion products were size-selected on an agarose gel, cutting below 150 bp. High-throughput sequencing libraries were prepared using 10 ng of size-selected material, using the Kapa Hyperprep kit as per manufacturer's instruction. Libraries were sequenced with 50 bp single-end reads on an Illumina HiSeq 2500 sequencer according to manufacturer's instructions

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

473962381

Reads aligned (%)

96.3

Duplicates removed (%)

81.5

Number of peaks

50739 (qval < 1E-05)

hg19

Number of total reads

473962381

Reads aligned (%)

95.6

Duplicates removed (%)

83.0

Number of peaks

50406 (qval < 1E-05)