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

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Item Type:Review
Title:A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics
Creators Name:Pennitz, P. and Kirsten, H. and Friedrich, V.D. and Wyler, E. and Goekeri, C. and Obermayer, B. and Heinz, G.A. and Mashreghi, M.F. and Büttner, M. and Trimpert, J. and Landthaler, M. and Suttorp, N. and Hocke, A.C. and Hippenstiel, S. and Tönnies, M. and Scholz, M. and Kuebler, W.M. and Witzenrath, M. and Hoenzke, K. and Nouailles, G.
Abstract: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 We compared the single-cell transcriptomes from publicly available and unpublished datasets of the lungs in six different species: human (Homo sapiens), African green monkey (Chlorocebus sabaeus), pig (Sus domesticus), hamster (Mesocricetus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.
Keywords:Base Sequence, Lung, Pulmonologists, Species Specificity, Transcriptome, Animals, Chlorocebus aethiops, Cricetinae, Mice, Rats, Swine
Source:European Respiratory Review
ISSN:0905-9180
Publisher:European Respiratory Society
Volume:31
Number:165
Page Range:220056
Date:30 September 2022
Official Publication:https://doi.org/10.1183/16000617.0056-2022
PubMed:View item in PubMed

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