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Series GSE156162 Query DataSets for GSE156162
Status Public on Nov 12, 2021
Title Single-cell transcriptional profiling of splenic fibroblasts reveals subset-specific innate immune signatures in homeostasis and during viral infection
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Our understanding of the composition and functions of splenic stromal cells remains incomplete. Here, based on analysis of over 20,000 single cell transcriptomes of splenic fibroblasts, we characterized the phenotypic and functional heterogeneity of these cells in a healthy state and during virus infection. We describe eleven transcriptionally distinct fibroblastic cell clusters, reassuring known subsets and revealing yet unascertained heterogeneity amongst fibroblasts occupying diverse splenic niches. We further identify striking differences in innate immune signatures of distinct stromal compartments in vivo. Compared to other fibroblasts and to endothelial cells, Ly6C+ fibroblasts of the red pulp showed enhanced interferon-stimulated gene expression in homeostasis, upon systemic interferon stimulation and during virus infection in vivo. Collectively, we provide an updated map of fibroblastic cell diversity in the spleen that suggests a specialized innate immune function for splenic red pulp fibroblasts.
 
Overall design Bulk RNA-seq of splenic stromal cells from uninfected and 24h post-infected mice. Single cell RNA-seq of splenic stromal cells from uninfected and 24h post-infected mice
 
Contributor(s) Pezoldt J, Wiechers C, Erhard F, Rand U, Bulat T, Beckstette M, Brendolan A, Beckstette M, Huehn J, Kalinke U, Mueller M, Strobl B, Deplancke B, Cicin-Sain L, Sitnik KM
Citation(s) 34857864
Submission date Aug 13, 2020
Last update date Jan 07, 2022
Contact name Joern Pezoldt
E-mail(s) jorn.pezoldt@epfl.ch
Phone 0041766040171
Organization name EPFL
Department SV
Lab Laboratory Systems Biology and Genetics
Street address Station 19, SV 3818.A
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (38)
GSM4725808 RPMC isolated from germ-free housed mice [RPMC_GF_1]
GSM4725809 RPMC isolated from germ-free housed mice [RPMC_GF_2]
GSM4725810 RPMC isolated from germ-free housed mice [RPMC_GF_3]
Relations
BioProject PRJNA656945
SRA SRP277338

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE156162_Expression_Foldchanges.xlsx 13.3 Mb (ftp)(http) XLSX
GSE156162_RCM_steadyState_1_CBs.txt.txt.gz 27.1 Mb (ftp)(http) TXT
GSE156162_RCM_steadyState_2_CBs.txt.txt.gz 28.0 Mb (ftp)(http) TXT
GSE156162_RCM_viralInfected_1_CBs.txt.txt.gz 31.3 Mb (ftp)(http) TXT
GSE156162_RCM_viralInfected_2_CBs.txt.txt.gz 33.8 Mb (ftp)(http) TXT
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Processed data are available on Series record
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