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Series GSE143920 Query DataSets for GSE143920
Status Public on Feb 12, 2020
Title Characterization of rat ILCs reveals ILC2 as the dominant intestinal subset
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Innate lymphoid cells (ILCs) are tissue-resident lymphocytes that lack antigen-specific receptors and exhibit innate effector functions such as cytokine production that play an important role in immediate responses to pathogens especially at mucosal sites. Mouse and human ILC subsets have been extensively characterized in various tissues and in blood. In this study, we present the first characterization of ILCs and ILC subsets in rat gut and secondary lymphoid organs. ScRNAseq and flow cytometric data shows that phenotype and function of rat ILC subsets are conserved similar to human and mouse ILCs. However, contrary to human and mouse, our study unexpectedly revealed that ILC2 and not ILC3 was by far the dominant ILC subset in the rat intestinal lamina propria. ILC2 predominance in the gut was independent of rat strain, sex or housing facility. In contrast, ILC3 were the main ILC subset in mesenteric lymph nodes and Peyer patches, in which strain-dependent differences in ILC frequencies were also observed. In conclusion, our study demonstrates that in spite of highly conserved phenotype and function between mice, rat and humans, the distribution of ILC subsets in the intestinal mucosa is species-dependent, likely in response to both genetic and environmental factors.
Overall design Single ILCs were sorted by flow cytometry for single cell RNAseq library preparation using Chromium Single Cell 3’ v3 Reagent Kit (10x Genomics)
Contributor(s) Abidi A, Thomas L, Gaëlle B, Laurence B, Cynthia F, Cédric L, Raja T, Jeremie P, Régis J, Jérôme M
Citation(s) 32140157
Submission date Jan 19, 2020
Last update date Mar 09, 2020
Contact name Ahmed Abidi
Organization name INSERM
Lab U1064 Centre de Recherche en Transplantation et Immunologie
Street address CHU Nantes - Hôtel Dieu 30 Bd Jean Monnet
City Nantes
State/province Loire Atlantique
ZIP/Postal code 44093
Country France
Platforms (1)
GPL20084 Illumina NextSeq 500 (Rattus norvegicus)
Samples (1)
GSM4276643 Colon Innate Lymphoid cells
BioProject PRJNA602155
SRA SRP243047

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Supplementary file Size Download File type/resource
GSE143920_RAW.tar 93.7 Mb (http)(custom) TAR (of MTX, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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