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A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics

Single-cell ribonucleic acid sequencing is becoming widely employed to study biological processes at a novel resolution depth. The ability to analyse transcriptomes of multiple heterogeneous cell types in parallel is especially valuable for cell-focused lung research where a variety of resident and...

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Autores principales: Pennitz, Peter, Kirsten, Holger, Friedrich, Vincent D., Wyler, Emanuel, Goekeri, Cengiz, Obermayer, Benedikt, Heinz, Gitta A., Mashreghi, Mir-Farzin, Büttner, Maren, Trimpert, Jakob, Landthaler, Markus, Suttorp, Norbert, Hocke, Andreas C., Hippenstiel, Stefan, Tönnies, Mario, Scholz, Markus, Kuebler, Wolfgang M., Witzenrath, Martin, Hoenzke, Katja, Nouailles, Geraldine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: European Respiratory Society 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9724811/
https://www.ncbi.nlm.nih.gov/pubmed/35896273
http://dx.doi.org/10.1183/16000617.0056-2022
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author Pennitz, Peter
Kirsten, Holger
Friedrich, Vincent D.
Wyler, Emanuel
Goekeri, Cengiz
Obermayer, Benedikt
Heinz, Gitta A.
Mashreghi, Mir-Farzin
Büttner, Maren
Trimpert, Jakob
Landthaler, Markus
Suttorp, Norbert
Hocke, Andreas C.
Hippenstiel, Stefan
Tönnies, Mario
Scholz, Markus
Kuebler, Wolfgang M.
Witzenrath, Martin
Hoenzke, Katja
Nouailles, Geraldine
author_facet Pennitz, Peter
Kirsten, Holger
Friedrich, Vincent D.
Wyler, Emanuel
Goekeri, Cengiz
Obermayer, Benedikt
Heinz, Gitta A.
Mashreghi, Mir-Farzin
Büttner, Maren
Trimpert, Jakob
Landthaler, Markus
Suttorp, Norbert
Hocke, Andreas C.
Hippenstiel, Stefan
Tönnies, Mario
Scholz, Markus
Kuebler, Wolfgang M.
Witzenrath, Martin
Hoenzke, Katja
Nouailles, Geraldine
author_sort Pennitz, Peter
collection PubMed
description Single-cell ribonucleic acid sequencing is becoming widely employed to study biological processes at a novel resolution depth. The ability to analyse transcriptomes of multiple heterogeneous cell types in parallel is especially valuable for cell-focused lung research where a variety of resident and recruited cells are essential for maintaining organ functionality. We compared the single-cell transcriptomes from publicly available and unpublished datasets of the lungs in six different species: human (Homo sapiens), African green monkey (Chlorocebus sabaeus), pig (Sus domesticus), hamster (Mesocricetus auratus), rat (Rattus norvegicus) and mouse (Mus musculus) by employing RNA velocity and intercellular communication based on ligand–receptor co-expression, among other techniques. Specifically, we demonstrated a workflow for interspecies data integration, applied a single unified gene nomenclature, performed cell-specific clustering and identified marker genes for each species. Overall, integrative approaches combining newly sequenced as well as publicly available datasets could help identify species-specific transcriptomic signatures in both healthy and diseased lung tissue and select appropriate models for future respiratory research.
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spelling pubmed-97248112022-12-08 A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics Pennitz, Peter Kirsten, Holger Friedrich, Vincent D. Wyler, Emanuel Goekeri, Cengiz Obermayer, Benedikt Heinz, Gitta A. Mashreghi, Mir-Farzin Büttner, Maren Trimpert, Jakob Landthaler, Markus Suttorp, Norbert Hocke, Andreas C. Hippenstiel, Stefan Tönnies, Mario Scholz, Markus Kuebler, Wolfgang M. Witzenrath, Martin Hoenzke, Katja Nouailles, Geraldine Eur Respir Rev Reviews Single-cell ribonucleic acid sequencing is becoming widely employed to study biological processes at a novel resolution depth. The ability to analyse transcriptomes of multiple heterogeneous cell types in parallel is especially valuable for cell-focused lung research where a variety of resident and recruited cells are essential for maintaining organ functionality. We compared the single-cell transcriptomes from publicly available and unpublished datasets of the lungs in six different species: human (Homo sapiens), African green monkey (Chlorocebus sabaeus), pig (Sus domesticus), hamster (Mesocricetus auratus), rat (Rattus norvegicus) and mouse (Mus musculus) by employing RNA velocity and intercellular communication based on ligand–receptor co-expression, among other techniques. Specifically, we demonstrated a workflow for interspecies data integration, applied a single unified gene nomenclature, performed cell-specific clustering and identified marker genes for each species. Overall, integrative approaches combining newly sequenced as well as publicly available datasets could help identify species-specific transcriptomic signatures in both healthy and diseased lung tissue and select appropriate models for future respiratory research. European Respiratory Society 2022-07-27 /pmc/articles/PMC9724811/ /pubmed/35896273 http://dx.doi.org/10.1183/16000617.0056-2022 Text en Copyright ©The authors 2022 https://creativecommons.org/licenses/by-nc/4.0/This version is distributed under the terms of the Creative Commons Attribution Non-Commercial Licence 4.0. For commercial reproduction rights and permissions contact permissions@ersnet.org (mailto:permissions@ersnet.org)
spellingShingle Reviews
Pennitz, Peter
Kirsten, Holger
Friedrich, Vincent D.
Wyler, Emanuel
Goekeri, Cengiz
Obermayer, Benedikt
Heinz, Gitta A.
Mashreghi, Mir-Farzin
Büttner, Maren
Trimpert, Jakob
Landthaler, Markus
Suttorp, Norbert
Hocke, Andreas C.
Hippenstiel, Stefan
Tönnies, Mario
Scholz, Markus
Kuebler, Wolfgang M.
Witzenrath, Martin
Hoenzke, Katja
Nouailles, Geraldine
A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics
title A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics
title_full A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics
title_fullStr A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics
title_full_unstemmed A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics
title_short A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics
title_sort pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics
topic Reviews
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9724811/
https://www.ncbi.nlm.nih.gov/pubmed/35896273
http://dx.doi.org/10.1183/16000617.0056-2022
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