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| Status |
Public on Sep 09, 2020 |
| Title |
Single Cell RNA sequencing of mouse SQ tumor from C57BL/6 with or with liver tumor. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The presence of liver tumor changes the transcriptome of SQ tumor-infiltrating adaptive and innate immune cells. We report differential transcriptomic changes within in the SQ tumor immune infiltrate of mice with and without concurrent liver tumor implantation within their livers. We show heatmap displaying the top 20 differentially expressed genes by SQ MDSC and Tregs between the two groups via scRNAseq. Violin plots showing the top 2 differentially upregulated genes by SQ Tregs from mice with liver tumor. Heatmap displaying the top 20 differentially upregulated genes by SQ CD8 T cells between the two groups. Violin plots showing differential expression of ICOS and CTLA-4 by SQ CD8 T cells between the two groups. Unbiased re clustering (UMAP) and stacked bar graph of relative frequencies of monocyte/myeloid cells showing 9 distinct scRNAseq subclusters. Violin plots showing relative MDSC score ordered by monocyte/myeloid cell subclusters. Our data suggests that mice with liver tumors have increased activation of Tregs, decreased activation of CD8 T cells and transcriptomic modifications within the MDSC compartment within their SQ tumors.
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| Overall design |
FACS-sorted live CD45+ tumor infiltrating cells from the subcutaneous tumor 14 days post implantation from SQ and SQ+Liver from 3 pooled mice. 2 independent experiments.
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| Contributor(s) |
Smith J, Lee JC |
| Citation(s) |
33008914 |
| |
| Submission date |
Sep 08, 2020 |
| Last update date |
Nov 07, 2024 |
| Contact name |
Jennifer Anne Smith |
| E-mail(s) |
jennifer.bridge@ucsf.edu
|
| Organization name |
University of California, San Francisco
|
| Department |
Diabetes Center
|
| Street address |
513 Parnassus Ave HS1102
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA662332 |
| SRA |
SRP281231 |
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