Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Blood

Cell type

Bone Marrow Cells

MeSH Description

Cells contained in the bone marrow including fat cells (see ADIPOCYTES); STROMAL CELLS; MEGAKARYOCYTES; and the immediate precursors of most blood cells.

Sample

source_name

Bone marrow

tissue

Bone marrow

cell type

CD45.2+LKFcgRII/III+CD55-

tumor stage

Leukemia

genotype

KLG-E

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Cells were sorted into lysis buffer containing TD tagmentation buffer (Illumina), 1% digitonin, 10% Tween 20 and PBS. After cells were sorted into the lysis buffer the Tn5 transposase was then added and immediately incubated at 30C for 30mins with an agitation at 300rpm. Samples were then purified using a Qiagen MinElute Kit . Samples were then PCR amplified and indexed using NEBNext High-Fidelity 2x PCR master mix and P7 and P5 primers containing Nextera adaptor sequences. Samples were sequenced on Illumina NextSeq 500 Instrument

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

16633658

Reads aligned (%)

96.3

Duplicates removed (%)

35.0

Number of peaks

56461 (qval < 1E-05)

mm9

Number of total reads

16633658

Reads aligned (%)

96.1

Duplicates removed (%)

35.2

Number of peaks

56381 (qval < 1E-05)