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

ENA first public
2018-09-30
ENA last update
2018-04-12
ENA-CHECKLIST
ERC000011
External Id
SAMEA1116800
INSDC center alias
Gordon and Jessie Gilmour Leukaemia Research Laboratory, QIMR Berghofer Medical Research Institute
INSDC center name
Gordon and Jessie Gilmour Leukaemia Research Laboratory, QIMR Berghofer Medical Research Institute
INSDC first public
2018-09-30T17:01:59Z
INSDC last update
2018-04-12T10:57:34Z
INSDC status
public
Submitter Id
E-MTAB-6649:lskjak2dnmt3a1
age
6 to 8
broker name
ArrayExpress
cell type
hematopoietic stem cell
common name
house mouse
disease
myeloproliferative disorder
disease staging
early
genotype
Jak2+/V617F; CRISPR/Cas9 mediated knockout of Dnmt3a
growth condition
transplanted for 8 weeks into C57BL/6 mice
organism part
bone marrow
phenotype
GFP+ LSK (Lin-,Sca1+,Kit+)
sample name
E-MTAB-6649:lskjak2dnmt3a1
sex
mixed
strain
C57BL/6

Sequenced DNA Library

library_name
lskjak2dnmt3a1_p
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
PCR
library_construction_protocol
Jak2VF LSK (Lin-, Sca-1 high, c-Kit high) were sorted, transduced with lentivirus coding Cas9 coupled to a GFP reporter with or without sg-RNA targeting Dnmt3a. After 36 hours cells were transplanted to C57BL6 recipients. Jak2VF-emp-Cas9 and Jak2VF-Dnmt3a-Cas9 GFP+ve LSKs were purified by flow cytometry and processed 8 weeks post transplantation. Jack2VF LSK cells are as described in Mullally A, Lane SW, Ball B, et al. Physiological Jak2V617F expression causes a lethal myeloproliferative neoplasm with differential effects on hematopoietic stem and progenitor cells. Cancer Cell. 2010; 17(6):584–596. [PubMed: 20541703]. FACS sorted GFP+ cells were washed in ice cold PBS, pelleted and lysed in 50ul of lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) NP40 ). The lysate was centrifuged at 500g for 10 mins. DNA tagmentation and library preparation was performed on the nuclei pellet using the Nextera DNA Library Prep Kit (Illumina).

Sequencing Platform

instrument_model
NextSeq 550

mm10

Number of total reads
52074241
Reads aligned (%)
91.7
Duplicates removed (%)
12.5
Number of peaks
105123 (qval < 1E-05)

mm9

Number of total reads
52074241
Reads aligned (%)
91.6
Duplicates removed (%)
12.6
Number of peaks
104800 (qval < 1E-05)

Base call quality data from DBCLS SRA