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Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [scRNA-Seq]

ABSTRACT: Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [scRNA-Seq]

PROVIDER: PRJNA719853 | ENA |

REPOSITORIES: ENA

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	SRR14146526.fastq.gz	Fastqsanger.gz

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Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [scRNA-Seq]

Project description:Although multiple studies have investigated the mesenchymal stem and progenitor cells (MSCs) that give rise to mature bone marrow, high heterogeneity in their morphologies and properties causes difficulties in molecular separation of their distinct populations. In this study, by taking advantage of the resolution of the single cell transcriptome, we analyzed Sca-1 and PDGFR-α fraction in the mouse bone marrow tissue. The single cell transcriptome enabled us to further classify the population into seven populations according to their gene expression profiles. We then separately obtained the seven populations based on candidate marker genes, and specified their gene expression properties and epigenetic landscape by ATAC-seq. Our findings will enable to elucidate the stem cell niche signal in the bone marrow microenvironment, reconstitute bone marrow in vitro, and shed light on the potentially important role of identified subpopulation in various clinical applications to the treatment of bone- and bone marrow-related diseases.

2021-05-22 | GSE171530 | GEO

Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties

Project description:Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties

| PRJNA719851 | ENA

Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [RNA-Seq]

Project description:Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [RNA-Seq]

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Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [ATAC-Seq]

Project description:Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [ATAC-Seq]

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Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties [RNA-Seq]

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Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties.

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Endothelium-derived stromal cells contribute to bone marrow niche formation

Project description:Comprehensive transcriptional characterization of bone marrow stromal cells by RNA sequencing was performed to determine the molecular properties/signatures of endothelium during niche formation.Here, we identify a rare subset of cells in the human fetal BM that co-express endothelial and stromal markers, including low-affinity nerve growth factor receptor (LNGFR/CD271). They display transcriptional reprogramming consistent with endothelial-to-mesenchymal transition (EndoMT), reflected in their potential to generate stromal cells with in vivo BM niche forming capacity.

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Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-05-22 | GSE171531 | GEO

Single-cell dissection of Comma-1D cultures reveals cell populations with unique differentiation and transformation properties [scRNA-Seq]

Project description:The mammary epithelial tree is a heterogeneous structure that contains two main populations, luminal and basal, with distinct molecular and functional characteristics. The investigation of how this heterogeneity is developed and how it influences breast tumorigenesis has been hampered by the need to perform these studies using animal models due to the lack of relevant, tractable, and fully characterized in vitro models. Comma-1D is an immortalized mouse mammary epithelial cell line that has unique morphogenetic properties particularly its ability to generate cells of luminal and basal lineages. Here, we perform single-cell RNA-seq studies to dissect its heterogeneous nature. Our analysis reveals that Comma-1D cultures consist of two main populations with luminal and basal features and a smaller population with mixed lineage and bipotent characteristics. Additionally, we demonstrate that multiple transcription factors associated with the differentiation of the mammary epithelium in vivo also modulate this process in Comma-1D cultures. Finally, we have used the Comma-1D model to study how the cellular subtype of origin influences the response to cancer-promoting mutations. We found that only cells with luminal molecular features were able to acquire transformed characteristics after an oncogenic HER2 mutant was introduced in their genomes. Overall, the studies present here characterize at a single-cell level the heterogeneity of the Comma-1D cell line and illustrate how the unique properties of Comma-1D cells can be used as an experimental model to study both the differentiation and the transformation processes in vitro.

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