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

Spleen day 8 after lethal irradiation and transplantation of unfractionated bone marrow cells

strain background

B6SJL

cell type

Splenic stress-BFU-E

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

For ATAC-seq: sorted cells were washed in ice cold PBS prior to Assay for Transposase Accessible Chromatin (ATAC-seq) library preparation was performed essentially as described by Buenrostro et al. 2013, using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers. Sequencing was performed on a NextSeq500 (Illumina, San Diego, CA, USA). RNA-seq libraries were constructed using SMARTer Stranded Total RNA-Seq Kit v2 (Pico Input Mammalian; Takara Bio USA, Mountain View, CA, USA) followed by sequencing on a HiSeq3000 (Illumina, San Diego, CA, USA)

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

91005710

Reads aligned (%)

72.2

Duplicates removed (%)

66.1

Number of peaks

56089 (qval < 1E-05)

mm9

Number of total reads

91005710

Reads aligned (%)

72.1

Duplicates removed (%)

66.2

Number of peaks

56709 (qval < 1E-05)