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Single-cell RNAseq of human bone marrow cells (Drop-seq)

ABSTRACT: Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Total bone marrow (TBM) and weakly lineage depleted bone marrow (DBM; CD235a and/or Cd45 negative) and stromal cells (STRO-1 positive or collagenase IV released) were analysed.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Ben MacArthur

PROVIDER: E-MTAB-8629 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing.

Stumpf Patrick S PS Du Xin X Imanishi Haruka H Kunisaki Yuya Y Semba Yuichiro Y Noble Timothy T Smith Rosanna C G RCG Rose-Zerili Matthew M West Jonathan J JJ Oreffo Richard O C ROC Farrahi Katayoun K Niranjan Mahesan M Akashi Koichi K Arai Fumio F MacArthur Ben D BD

Communications biology 20201204 1

Biomedical research often involves conducting experiments on model organisms in the anticipation that the biology learnt will transfer to humans. Previous comparative studies of mouse and human tissues were limited by the use of bulk-cell material. Here we show that transfer learning-the branch of machine learning that concerns passing information from one domain to another-can be used to efficiently map bone marrow biology between species, using data obtained from single-cell RNA sequencing. We ...[more]

PMID: 33277618

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Single-cell RNAseq of human bone marrow cells enriched for stromal and endothelial markers

Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Subsets of bone marrow cells were isolated using magnetic cell sorting to enrich for putative skeletal stem cells.

2021-06-30 | E-MTAB-9662 | biostudies-arrayexpress

Single-cell RNAseq of mouse bone marrow cells (Drop-seq)

Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Total bone marrow (TBM) and weakly depleted bone marrow (DBM; Ter119/Cd45 negative cells) were analysed.

2020-11-27 | E-MTAB-8630 | biostudies-arrayexpress

Single-cell RNAseq of human bone marrow cells enriched using RNA probes

Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Subsets of bone marrow cells were isolated using fluorescence-assisted cell sorting to enrich for putative skeletal stem cells.

2022-05-31 | E-MTAB-9664 | biostudies-arrayexpress

Mito-protective autophagy is impaired in erythroid cells of aged mtDNA-mutator mice

Project description:Somatic mitochondrial DNA (mtDNA) mutations contribute to the pathogenesis of age-related disorders, including myelodysplastic syndromes (MDS). The accumulation of mitochondria harboring mtDNA mutations in patients with these disorders suggests a failure of normal mitochondrial quality-control systems. The mtDNA-mutator mice acquire somatic mtDNA mutations via a targeted defect in the proofreading function of the mtDNA polymerase, PolgA, and develop macrocyticanemia similar to that of patients with MDS. We observed an unexpected defect in clearance of dysfunctional mitochondria at specific stages during erythroid maturation in hematopoietic cells from aged mtDNA-mutator mice. Mechanistically, aberrant activation of mechanistic target of rapamycin signaling and phosphorylation of uncoordinated 51-like kinase (ULK) 1 in mtDNA-mutator mice resulted in proteasome mediated degradation of ULK1 and inhibition of autophagy in erythroid cells. To directly evaluate the consequence of inhibiting autophagy on mitochondrial function in erythroid cells harboring mtDNA mutations in vivo, we deleted Atg7 from erythroid progenitors of wildtype and mtDNA-mutator mice. Genetic disruption of autophagy did not cause anemia in wild-type mice but accelerated the decline in mitochondrial respiration and development of macrocytic anemia in mtDNA-mutator mice. These findings highlight a pathological feedback loop that explains how dysfunctional mitochondria can escape autophagy-mediated degradation and propagate in cells predisposed to somatic mtDNA mutations, leading to disease. We used microarrays to identify expression profiles and pathways that are differentially activated or suppressed in Ter119+ bone marrow cells isolated from phlebotomized wildtype or Polg mutant mice

2015-04-21 | E-GEOD-57761 | biostudies-arrayexpress

Single-cell characterization of immune aplastic anemia reveals convergence of adaptive and innate immunity: in vitro

Project description:Immune aplastic anemia (AA) is a life-threatening bone marrow (BM) failure disorder driven by an autoimmune T cell attack against the hematopoietic stem and progenitor cells (HSPCs). However, the autoantigen targets and the role of other immune cells are unknown. Here, by combining scRNA+TCRαβ-seq, TCRβ-seq, flow cytometry and plasma cytokine profiling of >250 patients with AA, >250 patients with other hematological disorders and >1,000 healthy controls, we identify NK cells and CD8+ TEMRA cells expressing NK receptors with AA-associated TCRB-seq motifs as the most dysregulated immune cell populations in AA BM. Functional co-culture experiments with scRNA-TCRαβ-seq readout utilizing primary HSPCs and immune cells (in total 55 conditions) provide evidence that NK cells alone cannot kill HSPCs, but sensitize them to CD8+ T cell mediated killing. Furthermore, HSPCs induce strong activation of T cell clones with CD8+ TEMRA NK-like phenotype and AA-associated TCR motifs. To conclude, our results reveal convergent evolution of innate and adaptive immune cells in AA, where NK cells support CD8+ T cell mediated autoimmunity.

2024-12-12 | E-MTAB-13484 | biostudies-arrayexpress

Cellular adhesion promotes prostate cancer cells escape from dormancy

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2015-10-26 | E-GEOD-64262 | biostudies-arrayexpress

Hematopoietic Transcriptional Comparison of HSC from B10.BR/JRep and B10.BR/J (drifted) mice

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2009-09-15 | E-GEOD-17471 | biostudies-arrayexpress

scRNAseq for bone marrow cells from Cebpαcre/+ R26EYFP/+ SbdsF/F (neutropenia) mice vs Cebpαcre/+ R26EYFP/+ Sbds+/+ (Ctrl) mice

Project description:To delineate the potential molecular mechanisms underlying the communication between neutrophils and NK cells, we performed scRNAseq of the neutropenic bone marrow (12 months after transplantation of Cebpacre/+ Sbds +/+ or F/F cells). To this end, bone marrow cells were subsorted into HSC+MPP (LKS CD48-), HPC1 (LKS CD48+CD150-), B and T cells (B220+, CD3+), NK cells (NK1.1+ NKp46+) and a myeloid ‘rest’ fraction (B220-,CD3-,NKp46- and NK1.1-) and sorted fractions pooled together to obtain robust representation of all bone marrow cell types in the scRNAseq data

2022-12-31 | E-MTAB-12428 | biostudies-arrayexpress

Combined miRNA and mRNA analysis of CD133(+) and CD34(+) cells

Project description:Microarray and miRNA analysis of CD133(+), CD34(+)CD133(-) and CD133(-)CD34(-) cells The goal of the experiment was the comparison of expression levels of mRNA and miRNA in CD133(+) and CD34(+)CD133(-) cells The RNA of CD133(+), CD34(+)CD133(-) and CD133(-)CD34(-) bone marrow cells was amplified by using the µMACSTM SuperAmpTM Kit (Miltenyi Biotec).

2011-03-14 | E-GEOD-22460 | biostudies-arrayexpress

Mass spectrometry-based analysis of Muse cells from different origins

Project description:Multilineage-differentiating stress enduring (Muse) cells are nontumorigenic endogenous pluripotent-like stem cells easily collected from various adult or fetal tissues. The tissue regenerative effects of Muse cells have been demonstrated in many disease models, as they reach damaged sites after intravenous injection to exert pleiotropic effects. Previous reports indicate that several human tissues are readily accessible for Muse cell isolation, including adult tissues such as bone marrow (BM) and embryonic tissues such as Wharton’s Jelly (WJ) from umbilical cord. Wa analyzed the protein repertoires of WJ-Muse and BM-Muse using mass spectrometry-based proteomics.

2023-07-17 | PXD036883 | Pride

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