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| Status |
Public on Feb 15, 2022 |
| Title |
TCR Sequences Lane 2 |
| Sample type |
SRA |
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| Source name |
CD8+ TIL
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| Organism |
Mus musculus |
| Characteristics |
celltype: CD8+ T Cell
strain: C57BL/6
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| Treatment protocol |
Female C57BL/6 mice from Taconic were inoculated with 106 B16F10 cells subcutaneously on the right flank. At day 8, mice received AIP therapy, followed by ICB every three days thereafter. On day 26, mice were euthanized.
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| Growth protocol |
B16F10 cells were cultured in Dulbecco’s Modified Eagle’s Medium (ATCC) supplemented with 10% fetal bovine serum (FBS, R&D Systems), 100 U/mL penicillin (Thermo), and 100 μg/mL streptomycin (Thermo).
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| Extracted molecule |
total RNA |
| Extraction protocol |
On day 26, mice were euthanized. Single cell suspensions were generated from tumors and spleens. Pan-T cell isolations were performed using an EasySep mouse T cell isolation kit (Stem Cell), and then T cells from three tumors were pooled and stained with Zombie Aqua, Fc block, 5 nM p15E-tetramer (produced in-house), CD3, and CD8. Splenocytes were used as controls for sorting.
Seq-Well
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Raw read processing was performed as in Macosko et al.
Briefly, sequencing reads were aligned to the mm10 reference genome, collapsed by unique molecular identifier (UMI) and aggregated by cell barcode to obtain a gene expression matrix of cells versus genes
Barcodes with under 300 unique genes detected were then excluded from analysis.
Genome_build: mm10
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| Submission date |
Feb 15, 2022 |
| Last update date |
Feb 15, 2022 |
| Contact name |
Duncan Matthew Morgan |
| E-mail(s) |
dmmorgan@mit.edu
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| Organization name |
MIT
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| Department |
Koch Institute
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| Lab |
Love lab
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| Street address |
500 Main St
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| City |
CAMBRIDGE |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE196782 |
Identification of highly cross-reactive mimotopes for a public T cell response in murine melanoma |
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| Relations |
| BioSample |
SAMN25976673 |
| SRA |
SRX14191108 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5900887_TCRLane2.tab.gz |
12.2 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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