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
long-term hematopoietic stem cells (LT-HSCs)
genotype
RUNX1 methylation-deficient

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
LT-HSCs were sorted and lysed in lysis buffer (10mM Tris-Cl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630). Chromatin was extracted and processed for Tn5 transposase-mediated tagmentation and adapter incorporation for 30 min at 37 °C using the Nextera DNA Library Prep Kit (Illumina) according to the manufacturer's protocol. Transposed DNA was amplified using NEBNext High-Fidelity 2× Master Mix (New England Biolabs). Samples were pooled and run on an Illumina HiSeq.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
34599469
Reads aligned (%)
68.8
Duplicates removed (%)
34.0
Number of peaks
39443 (qval < 1E-05)

mm9

Number of total reads
34599469
Reads aligned (%)
68.7
Duplicates removed (%)
34.0
Number of peaks
39427 (qval < 1E-05)

Base call quality data from DBCLS SRA