Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing
(1) Background: mouse models are fundamental to the study of hematopoiesis, but comparisons between mouse and human in single cells have been limited in depth. (2) Methods: we constructed a single-cell resolution transcriptomic atlas of hematopoietic stem and progenitor cells (HSPCs) of human and mo...
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MDPI AG
2021-04-01
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| Online Access: | https://www.mdpi.com/2073-4409/10/5/973 |
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| author | Shouguo Gao Zhijie Wu Jeerthi Kannan Liza Mathews Xingmin Feng Sachiko Kajigaya Neal S. Young |
| author_facet | Shouguo Gao Zhijie Wu Jeerthi Kannan Liza Mathews Xingmin Feng Sachiko Kajigaya Neal S. Young |
| author_sort | Shouguo Gao |
| collection | DOAJ |
| description | (1) Background: mouse models are fundamental to the study of hematopoiesis, but comparisons between mouse and human in single cells have been limited in depth. (2) Methods: we constructed a single-cell resolution transcriptomic atlas of hematopoietic stem and progenitor cells (HSPCs) of human and mouse, from a total of 32,805 single cells. We used Monocle to examine the trajectories of hematopoietic differentiation, and SCENIC to analyze gene networks underlying hematopoiesis. (3) Results: After alignment with Seurat 2, the cells of mouse and human could be separated by same cell type categories. Cells were grouped into 17 subpopulations; cluster-specific genes were species-conserved and shared functional themes. The clustering dendrogram indicated that cell types were highly conserved between human and mouse. A visualization of the Monocle results provided an intuitive representation of HSPC differentiation to three dominant branches (Erythroid/megakaryocytic, Myeloid, and Lymphoid), derived directly from the hematopoietic stem cell and the long-term hematopoietic stem cells in both human and mouse. Gene regulation was similarly conserved, reflected by comparable transcriptional factors and regulatory sequence motifs in subpopulations of cells. (4) Conclusions: our analysis has confirmed evolutionary conservation in the hematopoietic systems of mouse and human, extending to cell types, gene expression and regulatory elements. |
| first_indexed | 2024-03-10T12:06:40Z |
| format | Article |
| id | doaj.art-5a60be72a4c045ef84ece32e036f2535 |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-10T12:06:40Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-5a60be72a4c045ef84ece32e036f25352023-11-21T16:31:56ZengMDPI AGCells2073-44092021-04-0110597310.3390/cells10050973Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA SequencingShouguo Gao0Zhijie Wu1Jeerthi Kannan2Liza Mathews3Xingmin Feng4Sachiko Kajigaya5Neal S. Young6Hematology Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892, USAHematology Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892, USAHematology Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892, USAHematology Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892, USAHematology Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892, USAHematology Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892, USAHematology Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA(1) Background: mouse models are fundamental to the study of hematopoiesis, but comparisons between mouse and human in single cells have been limited in depth. (2) Methods: we constructed a single-cell resolution transcriptomic atlas of hematopoietic stem and progenitor cells (HSPCs) of human and mouse, from a total of 32,805 single cells. We used Monocle to examine the trajectories of hematopoietic differentiation, and SCENIC to analyze gene networks underlying hematopoiesis. (3) Results: After alignment with Seurat 2, the cells of mouse and human could be separated by same cell type categories. Cells were grouped into 17 subpopulations; cluster-specific genes were species-conserved and shared functional themes. The clustering dendrogram indicated that cell types were highly conserved between human and mouse. A visualization of the Monocle results provided an intuitive representation of HSPC differentiation to three dominant branches (Erythroid/megakaryocytic, Myeloid, and Lymphoid), derived directly from the hematopoietic stem cell and the long-term hematopoietic stem cells in both human and mouse. Gene regulation was similarly conserved, reflected by comparable transcriptional factors and regulatory sequence motifs in subpopulations of cells. (4) Conclusions: our analysis has confirmed evolutionary conservation in the hematopoietic systems of mouse and human, extending to cell types, gene expression and regulatory elements.https://www.mdpi.com/2073-4409/10/5/973hematopoiesisgene regulatory networksingle-cell RNA sequencingcross-species analysis |
| spellingShingle | Shouguo Gao Zhijie Wu Jeerthi Kannan Liza Mathews Xingmin Feng Sachiko Kajigaya Neal S. Young Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing Cells hematopoiesis gene regulatory network single-cell RNA sequencing cross-species analysis |
| title | Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing |
| title_full | Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing |
| title_fullStr | Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing |
| title_full_unstemmed | Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing |
| title_short | Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing |
| title_sort | comparative transcriptomic analysis of the hematopoietic system between human and mouse by single cell rna sequencing |
| topic | hematopoiesis gene regulatory network single-cell RNA sequencing cross-species analysis |
| url | https://www.mdpi.com/2073-4409/10/5/973 |
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