GSM4148645: Control MPP ATAC-seq 1; Mus musculus; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Unclassified
Cell type
Unclassified
NA
NA
Attributes by original data submitter
Sample
source_name
Multipotent Progenitor
strain
C57BL/6
genotype
Wild-type
age
8-weeks
cre-driver
Vav
cell type
Multipotent Progenitor
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).