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| Status |
Public on Mar 26, 2021 |
| Title |
Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes [scRNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: In this study, we show that mutations of the splicing factor SF3B1 in uveal melanoma (UM) generate immunogenic neo-antigens.
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| Overall design |
Thawed PBMC from patient UM1 were stained with PE and APC tetramers loaded with peptide 37, then tetramer positive cells were positively enriched using anti-APC and anti-PE microbeads (Miltenyi Biotech), stained with CD3 A700 and CD8 FITC and finally with DAPI. The positive fraction was sorted in a FACS ARIA (BD). To combine 5 tetramer positive populations from 2 donors (14, 17, 26 and 37 for UM2 and 18 for UM3) the tetramers were prepared using 5 different TotalSeq-PE streptavidins (BioLegend) and 1 classical fluorochrome-streptavidin (APC, PE-CF594, PE-Cy5, PE-Cy7), PE-CF594 was used for UM3 who had only one population sorted. The PBMC were stained with the 4 pairs of tetramers for patient UM2 and 1 pair of tetramers for patient UM3, enriched with anti PE-microbeads (Milteny Biotech), stained with CD3 A700 and CD8 FITC and DAPI and sorted separately. The cells were then counted, mixed and loaded onto a Chromium controller using Chromium next GEM Single Cell V(D)J reagent kit with feature barcoding technology according to manufacturer’s instructions
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| Contributor(s) |
Bigot J, Lalanne AI, Gueguen P |
| Citation(s) |
33811047 |
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| Submission date |
Mar 25, 2021 |
| Last update date |
Apr 04, 2021 |
| Contact name |
Paul Gueguen |
| E-mail(s) |
paul.gueguen@unil.ch
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| Organization name |
Institut Curie
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| Department |
Inserm U932
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| Street address |
26 rue D'Ulm
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| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE169610 |
Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes |
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| Relations |
| BioProject |
PRJNA717188 |
| SRA |
SRP312102 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE169609_RAW.tar |
148.9 Mb |
(http)(custom) |
TAR (of RDS, TAR) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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