Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Blood

Cell type

Hematopoietic Stem Cells

MeSH Description

Progenitor cells from which all blood cells derived. They are found primarily in the bone marrow and also in small numbers in the peripheral blood.

Sample

source_name

LT-HSC sorted from aged mouse (daughter cell)

strain

B6.SJL mice

tissue

Long-term Hematopoietic stem cells (LT-HSC)

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

cells were separated by pipetting and singularly subjected to fragmentation of open chromatin-regions using Tn5 transposase (Illumina), followed by a pre-amplification step, library preparation and subsequent paired-end sequencing. For the pre-amplification step, NEBNext Ultra II Q5 Master Mix was used with Primer 1: 5'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG3' and Primer 2: 5'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG3'. For dual-indexing, 10 μL of the pre-amplified ATAC reaction was used as input for Nextera index kit (Illumina). The generated libraries were quantified using agilent bio-analyzer and qPCR kit (New England Biolabs).

Sequencing Platform

instrument_model

Illumina HiSeq 3000

mm10

Number of total reads

4506371

Reads aligned (%)

10.3

Duplicates removed (%)

63.6

Number of peaks

30 (qval < 1E-05)

mm9

Number of total reads

4506371

Reads aligned (%)

10.3

Duplicates removed (%)

63.6

Number of peaks

24 (qval < 1E-05)