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Series GSE168333 Query DataSets for GSE168333
Status Public on Nov 24, 2023
Title Reassessing endothelial-to-mesenchymal transition in postnatal mouse bone marrow using single-cell RNA sequencing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Conflicting reports exist on whether endothelial cells (ECs) serve as a source of bone marrow stromal cells (BMSCs). In studies concerning the endothelial-to-mesenchymal transition (EndoMT), ECs expressing mesenchymal markers, as well as BMSCs expressing endothelial markers, are typically considered intermediates of EndoMT. To understand the lineage relationship between ECs and BMSCs in postnatal mouse bone marrow, we performed single-cell RNA sequencing (scRNA-seq) on ECs and BMSCs obtained from 5-week-old wild-type C57BL/6J mice, and analyzed the potential intermediates of EndoMT. Subsequently, BMSC and EC lineage tracing models, flow cytometry, and immunostaining techniques were used to validate the findings from scRNA-seq analysis.
Overall design We profiled bone marrow cells from mouse tibiae and femurs using scRNA-seq. Overall, bone marrow cells and bone fragments from tibiae and femurs of 5-week-old wild-type C57BL/6J mice were collected and digested with a mixture of collagenase, dispase and DNase. Subsequently, samples were subjected to lineage positive cell depletion by magnetic- and fluorescence-activated cell sorting (MACS/FACS). Cells positive for B220, Ter119, Gr-1, CD11b, CD3e, CD45, CD71, CD3, CD19 were depleted. Finally, we analyzed ECs expressing mesenchymal markers Prrx1, Lepr, Pdgfra, and Col1a1, as well as BMSCs expressing endothelial markers Pecam1, Cdh5, Tek, and Emcn in the scRNA-seq analysis.
Contributor(s) Xie H
Citation(s) 38123537
Submission date Mar 05, 2021
Last update date Jan 03, 2024
Contact name Hui Xie
Organization name Central South University
Department Orthopedics
Lab Xie
Street address #87 Xiangya Road
City changsha
State/province hunan
ZIP/Postal code 410008
Country China
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (2)
GSM5136346 bo scRNAseq
GSM5136347 bm scRNAseq
BioProject PRJNA706949
SRA SRP309458

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Supplementary file Size Download File type/resource
GSE168333_RAW.tar 189.0 Mb (http)(custom) TAR (of TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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