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
Bone Marrow
cell type
haematopoietic stem cell
mouse phenotype
Control
treatment
None
Sex
male
background strain
C57Bl/6
stimulation
Unstimulated

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Nuclei from 50,000 cells per replicate were isolated and lysed (10 mmol/L Tris-Cl (pH 7.4), 10 mmol/L NaCl, 3 mmol/L MgCl2, 0.05% NP-40) on ice. Isolated nuclei were put through transposition reaction using Tn5 transposase and TD buffer (Illumina, USA) and DNA purified with MinElute PCR Purification Kit (Qiagen). Library amplification (NEBNext High Fidelity 2x PCR master mix, New England Biolabs, USA) was performed using cutom Nextera primers, followed by SPRI size selection to exclude fragments larger than 1,200 bp. Libraries were sequenced using the Illumina HiSeq 3000/4000 platform and the 50-bp single-read configuration.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
42946519
Reads aligned (%)
91.2
Duplicates removed (%)
41.6
Number of peaks
47431 (qval < 1E-05)

mm9

Number of total reads
42946519
Reads aligned (%)
91.1
Duplicates removed (%)
41.6
Number of peaks
47387 (qval < 1E-05)

Base call quality data from DBCLS SRA