|
| 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.
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| |
|
| 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.
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| |
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| 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) |
|
| Relations |
| BioProject |
PRJNA449452 |
| SRA |
SRP139262 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
