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
HSC KSL Flt3-
treatment
no LPS
cell type
Lin- Sca+ Kit- Flt3- bone marrow
strain
C57BL/6

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
40-50 000 sorted HSC KSL Flt3- from pool of 4-8 mice were lyzed in lysis buffer. After centrifugation, nuclei were resuspend in reaction buffer containing Tn5 transposase. Tagmented DNA was purified using SPRI beads. Library amplification using nextera kit has been done as described in Lara-Astiaso et al., 2014.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
4453637
Reads aligned (%)
97.3
Duplicates removed (%)
7.3
Number of peaks
7623 (qval < 1E-05)

mm9

Number of total reads
4453637
Reads aligned (%)
97.2
Duplicates removed (%)
7.5
Number of peaks
7516 (qval < 1E-05)

Base call quality data from DBCLS SRA