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
strain
C57BL/6
cell type
Normal HSPCs
group
control

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Briefly, 50,000 cells were lysed in lysis buffer (10mM Tirs-HCl, PH7.4, 10mM NaCl, 3mM MgCl2, 0.1%(v/v) IGPAL CA-630) for 10min on ice before centrifuged at 500g for 5min. The nuclei were added with 50ul transposition reaction buffer (5μL TruePrep Tagment Enzyme,10μL TruePrep Tagment Buffer L and 35μL ddH2O from Vazyme TD501-01) and followed with incubation at 37oC for 30min. After tagmentation, VAHTS DNA Clean Beads were used to stop the reaction and DNA was purified for final library construction (TruePrepTM DNA Library Prep Kit V2 for Illumina) before paired-end high-throughput sequencing using HiSeq XTen.

Sequencing Platform

instrument_model
HiSeq X Ten

mm10

Number of total reads
58315850
Reads aligned (%)
64.9
Duplicates removed (%)
48.6
Number of peaks
4260 (qval < 1E-05)

mm9

Number of total reads
58315850
Reads aligned (%)
64.8
Duplicates removed (%)
48.6
Number of peaks
4212 (qval < 1E-05)

Base call quality data from DBCLS SRA