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Series GSE169603 Query DataSets for GSE169603
Status Public on Mar 26, 2021
Title Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes [scTCR-seq]
Organism Homo sapiens
Experiment type Other
Summary Purpose: In this study, we show that mutations of the splicing factor SF3B1 in uveal melanoma (UM) generate immunogenic neo-antigens.
 
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
 
Contributor(s) Bigot J, Lalanne AI, Gueguen P
Citation(s) 33811047
Submission date Mar 25, 2021
Last update date Apr 04, 2021
Contact name Paul Gueguen
E-mail(s) paul.gueguen@unil.ch
Organization name Institut Curie
Department Inserm U932
Street address 26 rue D'Ulm
City Paris
ZIP/Postal code 75005
Country France
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (2)
GSM5210599 UM1 [scTCR-seq]
GSM5210600 UM2_3 [scTCR-seq]
This SubSeries is part of SuperSeries:
GSE169610 Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes
Relations
BioProject PRJNA717180
SRA SRP312087

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE169603_RAW.tar 350.0 Kb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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