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
Dnmt3a-KO
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
For RNA-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-) and Rps (Lin-, cKit+, Sca1+, C-150- CD48+) were sorted from a pooled sample of 2 male and 2 female 8-week old mice HSCs were purified from three or four biological replicates (composed of pooled WBM from three male and three female mice) of either Vav-CRE: Dnmt3a+/+; Tet2+/+ or Vav-CRE:Dnmt3afl/fl or + or Vav-CRE:Tet2fl/fl mice. Total RNA was isolated from the samples using the NucleoSpin RNA XS kit For RNA-seq, the SMARTer Ultra Low RNA kit (Clontech) was used to prepare the libraries from 3-5ng of total RNA. For ATAC-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-),MPPs ( Lin-, cKit+, Sca1+, C-150-, CD48-) and Rps (Lin-, cKit+, Sca1+, C-1-0+, CD+8-) were sorted from a pooled sample of 2 male and 2 female 8-week old mice HSCs were purified from three or four biological replicates (composed of pooled WBM from three male and three female mice) of either Vav-CRE: Dnmt3a+/+; Tet2+/+ or Vav-CRE:Dnmt3afl/fl or + or Vav-CRE:Tet2fl/fl mice. For ATAC-Seq, NEBNext High-Fidelity 2X PCR Master MIX (NEB M0541L) along with Nextera custom primers were used for library amplification of the ATAC DNA(5-7 cycles of PCR as determined by qPCR). Libraries were again purified with Ampure XP beads and run on an Illumina Hiseq 3000 (PE2X150) or NovaSeq(PE2x150).

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

mm10

Number of total reads
110412970
Reads aligned (%)
60.7
Duplicates removed (%)
48.0
Number of peaks
44727 (qval < 1E-05)

mm9

Number of total reads
110412970
Reads aligned (%)
60.6
Duplicates removed (%)
48.0
Number of peaks
44689 (qval < 1E-05)

Base call quality data from DBCLS SRA