Manual cell selection in single cell transcriptomics using scSELpy supports the analysis of immune cell subsets
Copyright © 2023 Dedden, Wiendl, Müller, Neurath and Zundler..
Introduction: Single cell RNA sequencing plays an increasing and indispensable role in immunological research such as in the field of inflammatory bowel diseases (IBD). Professional pipelines are complex, but tools for the manual selection and further downstream analysis of single cell populations are missing so far.
Methods: We developed a tool called scSELpy, which can easily be integrated into Scanpy-based pipelines, allowing the manual selection of cells on single cell transcriptomic datasets by drawing polygons on various data representations. The tool further supports the downstream analysis of the selected cells and the plotting of results.
Results: Taking advantage of two previously published single cell RNA sequencing datasets we show that this tool is useful for the positive and negative selection of T cell subsets implicated in IBD beyond standard clustering. We further demonstrate the feasibility for subphenotyping T cell subsets and use scSELpy to corroborate earlier conclusions drawn from the dataset. Moreover, we also show its usefulness in the context of T cell receptor sequencing.
Discussion: Collectively, scSELpy is a promising additive tool fulfilling a so far unmet need in the field of single cell transcriptomic analysis that might support future immunological research.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:14 |
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| Enthalten in: |
Frontiers in immunology - 14(2023) vom: 24., Seite 1027346 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Dedden, Mark [VerfasserIn] |
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| Links: |
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| Themen: |
Chronic inflammation |
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| Anmerkungen: |
Date Completed 22.01.2024 Date Revised 22.01.2024 published: Electronic-eCollection Citation Status MEDLINE |
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| doi: |
10.3389/fimmu.2023.1027346 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM356828832 |
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| 245 | 1 | 0 | |a Manual cell selection in single cell transcriptomics using scSELpy supports the analysis of immune cell subsets |
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| 500 | |a Date Revised 22.01.2024 | ||
| 500 | |a published: Electronic-eCollection | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2023 Dedden, Wiendl, Müller, Neurath and Zundler. | ||
| 520 | |a Introduction: Single cell RNA sequencing plays an increasing and indispensable role in immunological research such as in the field of inflammatory bowel diseases (IBD). Professional pipelines are complex, but tools for the manual selection and further downstream analysis of single cell populations are missing so far | ||
| 520 | |a Methods: We developed a tool called scSELpy, which can easily be integrated into Scanpy-based pipelines, allowing the manual selection of cells on single cell transcriptomic datasets by drawing polygons on various data representations. The tool further supports the downstream analysis of the selected cells and the plotting of results | ||
| 520 | |a Results: Taking advantage of two previously published single cell RNA sequencing datasets we show that this tool is useful for the positive and negative selection of T cell subsets implicated in IBD beyond standard clustering. We further demonstrate the feasibility for subphenotyping T cell subsets and use scSELpy to corroborate earlier conclusions drawn from the dataset. Moreover, we also show its usefulness in the context of T cell receptor sequencing | ||
| 520 | |a Discussion: Collectively, scSELpy is a promising additive tool fulfilling a so far unmet need in the field of single cell transcriptomic analysis that might support future immunological research | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a chronic inflammation | |
| 650 | 4 | |a gut homing | |
| 650 | 4 | |a inflammatory bowel disease | |
| 650 | 4 | |a single cell RNA sequencing | |
| 650 | 4 | |a transcriptomics | |
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| 700 | 1 | |a Wiendl, Maximilian |e verfasserin |4 aut | |
| 700 | 1 | |a Müller, Tanja M |e verfasserin |4 aut | |
| 700 | 1 | |a Neurath, Markus F |e verfasserin |4 aut | |
| 700 | 1 | |a Zundler, Sebastian |e verfasserin |4 aut | |
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