{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13862"],"description":["Transcriptome of young HSCs (Lin-CD34+CD38-), young Progenitors (Lin-CD34+CD38+) and old HSCs (Lin-CD34+CD38-) isolated from bone marrow samples of healthy donors."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - cDNA libraries were generated using SMARTseq v4 (Takara Bio). For HSCs, 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.","Nucleic Acid Extraction - Cells were sorted into RNA lysis buffer (Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)) and then stored at -80οC 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.","Sequencing - Libraries underwent sequencing on the Illumina NovaSeq platform, generating 50 million reads depth with 100bp paired-end sequencing","Sample Collection - Human frozen bone marrow samples were thawed at 37oC and transferred to 10ml of thawing media (IMDM, 10% FCS, 1mM EDTA, 1:1000 DNase) and spun down for 8 min at 300g. Cells were resuspended in Stem Span and let for recovery in the incubator for 20 min. Cells were resuspended in 500ul antibody mix (Lin(CD3/14/16/19/20/56)-APC; CD38-Pe/Cy7, CD34-FITC*)  at 4oC for 45 min. Cells were washed with 0.9% NaCl and incubated with Zombie-Aqua (1:1000) for 10 min at RT. Cells were finally washed and resuspended in 0.9% NaCl and filtered for FACS sorting. Sorting was then performed using a FACS Aria III at the MPI FACS facility, Freiburg, Germany.  1000 cells of young HSCs/Progenitors and old HSCs were sorted in 4 and 7 biological replicates, respectively."],"figure_sub":["MINSEQE Score","Assays and Data","organisation","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"additional_accession":["E-MTAB-13863"],"pubmed_authors":["Maria-Eleni Lalioti","Mari Carmen Romero-Mulero","Noemie Karabacz","Nina Cabezas-Wallscheid","Karin Jaecklein"]},"is_claimable":false,"name":"Population RNA-seq of young hematopoietic stem cells (HSCs) vs young progenitors vs old HSCs isolated from human bone marrow","description":"Transcriptome of young HSCs (Lin-CD34+CD38-), young Progenitors (Lin-CD34+CD38+) and old HSCs (Lin-CD34+CD38-) isolated from bone marrow samples of healthy donors.","dates":{"release":"2025-05-20T00:00:00Z","modification":"2026-06-05T16:50:40.406Z","creation":"2024-02-27T22:43:56.579Z"},"accession":"E-MTAB-13862","cross_references":{"ENA":["ERP158168"],"Biostudies":["E-MTAB-13863"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}