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Series GSE112903 Query DataSets for GSE112903
Status Public on May 10, 2018
Title Single-cell RNA sequencing of lymph node stromal cells reveals niche-associated heterogeneity
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Stromal cells (SCs) establish the compartmentalization of lymphoid tissues critical to the immune response. However, the full diversity of lymph node (LN) SCs remains undefined. Using droplet-based single-cell RNA sequencing we identified 9 peripheral LNs non-endothelial SC subsets. Included are the established subsets Ccl19hi T-zone reticular cells (TRCs), marginal reticular cells, follicular dendritic cells (FDCs) and perivascular cells. We also identified Ccl19lo TRCs, likely including cholesterol-25-hydroxylase+ cells located at the T-zone perimeter, Cxcl9+ TRCs in the T-zone and interfollicular region, CD34+ SCs in the capsule and medullary vessel adventitia, indolethylamine N-methyltransferase+ SCs in the medullary cords and Nr4a1+ SCs in several niches. These data help define how transcriptionally distinct LN SCs support niche-restricted immune functions and they provide evidence that many SCs are in an activated state.
Overall design Droplet-based scRNAseq on sorted mouse pLN CD45- CD31- cells from uninfected mice and mice at day 15 post-infection with LCMV-Armstrong.
Contributor(s) Rodda LB, Cyster JG
Citation(s) 29752062
Submission date Apr 10, 2018
Last update date Mar 19, 2019
Contact name Jason Cyster
Organization name University of California, San Francisco
Department Microbiology and Immunology
Lab Jason Cyster
Street address HSE 1001/Cyster Lab/Box 0414, 513 Parnassus Ave.
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (2)
GSM3090973 Uninfected
GSM3090974 Post-infection
BioProject PRJNA449452
SRA SRP139262

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

Supplementary file Size Download File type/resource
GSE112903_Table_S1_Mean_Expression.xlsx 5.8 Mb (ftp)(http) XLSX
GSE112903_Table_S2_Ccl19hi_TRC_Ccl19lo_TRC_Cxcl9_TRC.xlsx 4.0 Mb (ftp)(http) XLSX
GSE112903_Table_S3_MRC.xlsx 1.4 Mb (ftp)(http) XLSX
GSE112903_Table_S4_PvC.xlsx 1.4 Mb (ftp)(http) XLSX
GSE112903_Table_S5_CD34+_SC.xlsx 1.4 Mb (ftp)(http) XLSX
GSE112903_Table_S6_Inmt+_SC.xlsx 1.4 Mb (ftp)(http) XLSX
GSE112903_Table_S7_Nr4a1+_SC.xlsx 5.0 Mb (ftp)(http) XLSX
GSE112903_Table_S8_FDC.xlsx 1.4 Mb (ftp)(http) XLSX
GSE112903_uninf_lcmv_genesVcells.txt.gz 217.0 Mb (ftp)(http) TXT
GSE112903_uninf_lcmv_metadata.xlsx 1.3 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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