ChIP-Atlas: ERX2531453

ERX2531453
NextSeq 550 paired end sequencing; ATAC-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls 8 weeks post transplantation

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.

ENA first public: 2018-09-30
ENA last update: 2018-04-12
ENA-CHECKLIST: ERC000011
External Id: SAMEA1116801
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:lskjak2dnmt3a2
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:lskjak2dnmt3a2
sex: mixed
strain: C57BL/6

library_name: lskjak2dnmt3a2_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).