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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 29, 2024 |
| Title |
scRNAseq analysis of mouse draining lymph nodes during Ross River virus or LCMV infection |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The aim of this study was to compare murine immune responses, particularly CD8+ T cell activation, in acute infection of either Ross River virus (RRV) or lymphocytic choriomeningitis virus (LCMV). LCMV induces a strong CD8+ T cell response that is required for viral clearance. RRV induces CD8+ T cells that only affect viral clearance in certain tissue and do not contribute to prevention of viral RNA persistence in lymphoid and joint-associated tissue. We sequenced cells from the draining lymph node at 5 days post infection to assess activation states of CD8+ T cells at this timepoint.
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| Overall design |
To study immune responses in the draining lymph node after viral infection, with a focus on CD8+ T cell activation, three samples were generated: naive, RRV, and LCMV. Wild type mice each received adoptive transfer of 1 x 10^6 CD8+ T cells from a P14 transgenic mouse (specific for the gp33 epitope naturally found in LCMV and genetically expressed by RRV-gp33) and were then inoculated in the footpad with 10^3 infectious units of RRV-gp33 or LCMV. Five days post infection, draining lymph nodes (popliteal) were harvested from the infected mice and also uninfected wild type and P14 transgenic mice as a naive control. Cells from 7 mice were pooled for each group: naive, RRV, and LCMV. A portion of each sample was enriched for transgenic CD8+ T cells by magnetic bead negative selection and fluorescence-activated cell sorting and added back to the bulk sample at a 1:4 ratio. Libraries were prepared from 20,000 cells from each sample using a 10x Genomics Chromium Single Cell 5' Reagent Kit v2 with TCR enrichment and sequenced.
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| Contributor(s) |
Christopher BB, Leran W, Brian WC, Ngan W, Ray OA, Tian-tian LT, Bjoern P, Kenneth MM, Scott HA, Thomas ME, Michael DS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Aug 29, 2024 |
| Last update date |
Aug 30, 2024 |
| Contact name |
Scott Handley |
| E-mail(s) |
shandley@wustl.edu
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| Organization name |
Washington University in St.Louis
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| Street address |
660 S Euclid Ave
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| City |
St.Louis |
| State/province |
MO |
| ZIP/Postal code |
63105 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA1153994 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE275970_RAW.tar |
217.9 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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