Antigen

Antigen Class

DNase-seq

Antigen

DNase-Seq

Cell type

Cell type Class

Blood

Cell type

CD34+ cells

NA

NA

Sample

source_name

CD34 positive AML cells from peripheral blood

condition

AML

Sequenced DNA Library

library_strategy

DNase-Hypersensitivity

library_source

GENOMIC

library_selection

DNase

library_construction_protocol

Cells were thawed in a water bath at 22C for 2 minutes, prior to addition of 120ul of DNaseI buffer consisting of 60nM KCL, 15 mM NaCl and 5 mM MgCL2. Digests were performed by adding 150 uL of DNaseI buffer equilibrated at 22C, containing 0.4% Nonidet P40 (or IGEPAL CA-630), 2 mM CaCl2, and either 1.5, 3 or 5 units/mL of Worthington DPFF DNase I. The permeabilized cells were digested for exactly 3 minutes at 22C, with occasional tapping to keep tubes in suspension, and lysed by addition of 300uL of 0.3 M NA Acetate, 10 mM EDTA pH 7.4, 1% SDS and 1 mg/Ml proteinase K. DNA was purified, size-selected, and processed for DNA-Seq with a MicroPlex library preparation kit v2 (Diagenode)

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

332677934

Reads aligned (%)

92.8

Duplicates removed (%)

85.0

Number of peaks

91284 (qval < 1E-05)

hg19

Number of total reads

332677934

Reads aligned (%)

92.4

Duplicates removed (%)

85.7

Number of peaks

90805 (qval < 1E-05)