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

ATAC_LinNegBM_Stag2KO

cell type

lineage depleted bone marrow (LinNegBM)

genotype/variation

Stag2KO

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

Cells (1e4) were lysed and incubated with transposition reaction mix containing PBS, 1% Digitonin, Tween-20, and Transposase (llumina). Samples were incubated for 30 minutes at 37C in a thermomixer at 1000rpm. Prior to amplification, samples were concentrated with the DNA Clean and Concentrator Kit-5 (Zymo). Samples were eluted in 20uL of elution buffer and PCR-amplified using the NEBNext 2X Master Mix (NEB) for 10 cycles and sequenced on a HiSeq 2500 (Illumina).

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

63101625

Reads aligned (%)

96.3

Duplicates removed (%)

41.2

Number of peaks

37498 (qval < 1E-05)

mm9

Number of total reads

63101625

Reads aligned (%)

96.2

Duplicates removed (%)

41.3

Number of peaks

37507 (qval < 1E-05)