Sample information curated by ChIP-Atlas

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.

Attributes by original data submitter

Sample

source_name
hematopoietic stem cells
strain
C57BL/6
tissue
Bone marrow
genotype
WT(Med23floxp/flowp)

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Bone marrow HSCs from WT or Med23-dificient adult mice were isolated by cell sorting (LSKsCD150+CD34-CD48-). 5,000 sorted cells in FACS Buffer were pelleted by centrifugation at 500 RCF for 5 minutes at 4C in a pre-cooled fixed-angle centrifuge. 50 ul transposase mixture (25 ul of 2x TD buffer, 2.5 ul of TDE1, 0.5 ul of 1% digitonin, 22 ul of nuclease-free water) (Cat# FC-121-1030, Illumina; Cat# G9441, Promega) was added to the cells and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37°C for 30 minutes. Transposed DNA was purified using a QIAgen MinElute Reaction Cleanup kit (Cat# 28204) and purified DNA was eluted in 10 ul elution buffer (10 mM Tris-HCl, pH 8). Transposed fragments were amplified and purified as described previously with primers. Libraries were quantified using qPCR prior to sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
65279253
Reads aligned (%)
58.6
Duplicates removed (%)
86.9
Number of peaks
723 (qval < 1E-05)

mm9

Number of total reads
65279253
Reads aligned (%)
58.6
Duplicates removed (%)
86.9
Number of peaks
707 (qval < 1E-05)

Base call quality data from DBCLS SRA