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 Cell
strain
C57BL/6
genotype
Wild-type
age
8-weeks
cre-driver
Vav
cell type
Hematopoietic stem cell

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
1.0x104 HSCs were sorted into PBS+10% FBS, lyzed in ATAC-RSB buffer for 3-minutes, and then tagmented for 30-minutes at 37°C using the Nextera TD/Transposase NebNext with custom primers was used for library amplification of the ATAC DNA (12-14 cycles of PCR as determined by qPCR). Libraries were again purified with Ampure XP beads and run on an Illumina Hiseq 3000 (PE2X150).

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
66142705
Reads aligned (%)
73.2
Duplicates removed (%)
46.8
Number of peaks
12856 (qval < 1E-05)

mm9

Number of total reads
66142705
Reads aligned (%)
73.1
Duplicates removed (%)
46.8
Number of peaks
12809 (qval < 1E-05)

Base call quality data from DBCLS SRA