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| Status |
Public on Nov 21, 2023 |
| Title |
Single-cell mRNA sequencing and TCR sequencing of CD4+ T cells in a mouse model of cutaneos B16 melanoma |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
This study sought to identify transcriptional states of CD4+ T cells from melanoma-challenged skin, primary tumours and tumour-draining lymph nodes. TCR sequencing was performed to identify expanded clonotypes to infer tumour-antigen specificity. This study identified heterogeneous populations of melanoma-specific CD4+ T cells that are distinct in the different anatomical locations.
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| Overall design |
C57B/6 mice were challenged with B16.gD melanoma using the recently developed epicutaneous melanoma model (Park et al, Nature 2019). Melanoma-challenged skin and draining (brachial) lymph nodes from the same mice were harvested 8 days following inoculation. Primary tumours and tumour-draining (brachial) lymph nodes from tumour-bearing mice were harvested 20 days following inoculation. As a batch control, a brachial lymph node was harvested from a naive C57BL/6 mouse. Samples were stained simultaneously with antibodies for flow cytometry and TotalSeq-C hashtag antibodies (Biolegend). Samples were sorted on CD45.2+CD3+CD8-CD4+CD44+ cells except for the naïve lymph node (batch control) which was sorted on CD45.2+CD3+CD8-CD4+CD44-CD62L+. Day 8 skin and lymph node samples were pooled from 32 mice across two experiments. Day 20 tumour and lymph node samples were pooled from 4 mice in one experiment.
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| Contributor(s) |
Bawden EG, Gebhardt T, Schröder J |
| Citation(s) |
38241401 |
| Submission date |
May 09, 2023 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Jan Schroeder |
| E-mail(s) |
jsch@unimelb.edu.au
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| Organization name |
University of Melbourne
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| Department |
DMI
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| Lab |
CSI
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| Street address |
Peter Doherty Institute Melbourne
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| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3053 |
| Country |
Australia |
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| Platforms (2) |
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| Samples (9)
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| GSM7311296 |
Naive brachial lymph node (experiment 1) scRNA |
| GSM7311297 |
Naive brachial lymph node (experiment 1) scTCR |
| GSM7311298 |
Draining brachial lymph node, day 8 p.i. (experiment 1) scRNA |
| GSM7311299 |
Draining brachial lymph node, day 8 p.i. (experiment 1) scTCR |
| GSM7311300 |
Skin, day 8 p.i., (experiment 1) scRNA |
| GSM7311301 |
Skin, day 8 p.i., (experiment 1) scTCR |
| GSM7311302 |
skin, lymph node, tumour scRNA |
| GSM7311303 |
skin, lymph node, tumour HASH |
| GSM7311304 |
skin, lymph node, tumour scTCR |
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| Relations |
| BioProject |
PRJNA970728 |
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