2025-07-18
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114565867
External Id
Max Planck Institute of Immunobiology and Epigenetics (MPI-IE)
INSDC center name
2023-10-31T20:59:50Z
INSDC last update
public
INSDC status
ERS16596851
SRA accession
E-MTAB-13508:human_HSPC_DMSO_Ctrl_1
Submitter Id
ArrayExpress
broker name
hematopoietic stem and progenitor cell
cell_type
healthy
clinical history
not collected
collection date
human
common name
Protocols: Human HSPCs (Lineage negative, CD38 negative, CD34 positive) isolated from sternal bone marrow of myocardial infarction patients or control patients were sorted into low-attachment 96-well plates containing StemSpan SFEM II media (StemCell Technologies) supplemented with StemSpanª CD34+ Expansion Supplement (StemCell Technologies). For in vitro cultivation, at-RA (2.5 _M final concentration), 4-oxo-RA (2.5 _M final concentration), or the respective volume of DMSO was added to the culture medium. Cells were cultured for 72h prior to harvest for RNA extraction. After culturing the cells, the low-attachment 96-well plate was centrifuged at 400g for 5 minutes. The cell culture medium was carefully removed using a pipette, and the cells were subsequently extracted into lysis buffer (Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)). Cells were then stored at -80¡C until further use. RNA isolation was conducted using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) following the manufacturer's guidelines. DNAse treatment was carried out employing the RNase-Free DNase Set (Qiagen). The resulting total RNA was utilized for generating cDNA libraries. cDNA libraries were generated using SMARTseq v4 (Takara Bio). 13 cycles of amplification were performed. To produce uniquely- and dually-barcoded sequencing libraries from the cDNA libraries, the NEBNext Ultra II FS DNA library kit (NEB) was utilized. This involved fragmenting 5 ng of the cDNA library for 22.5 minutes, followed by adaptor ligation and library amplification using cycle numbers determined by amount of input material.
description
adult
developmental stage
normal
disease
not collected
geographic location (country and/or sea)
Patient 1
individual
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
bone marrow
organism part
Lineage negative, CD38 negative, CD34 positive
phenotype
Homo sapiens
scientific_name
human_HSPC_DMSO_Ctrl_1
title