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Series GSE252650 Query DataSets for GSE252650
Status Public on Apr 02, 2024
Title Single-cell RNA sequencing of T3 sarcoma tumors following treatment with CD8-mIL2, CTRL-not-alpha-mIL2, or anti-PD-1
Organism Mus musculus
Experiment type Other
Summary To assess treatment-induced changes of intratumoral CD8+ T cells in an unbiased manner, CD8+ TILs from T3 sarcomas were analyzed using single-cell RNA-sequencing (scRNAseq) 2 or 4 days after therapy with CD8-mIL2, CTRL-not-α-mIL2, anti-PD-1, or combinations thereof. Barcoded peptide:MHC reagents were included to identify mLama4-specific CD8+ T cells. CD8-mIL2 therapy promotes the generation of a new stem-like effector CD8+ T cell cluster with a signature indicative of polyfunctionality and with features of T cell memory.
 
Overall design T3 tumor-bearing mice were treated on day twelve post-tumor transplant. Two and four days later, single-cell suspensions were prepared from TILs. Total CD8+ T cells were enriched using a CD8+ T cell positive selection kit (Miltenyi). Tumors from individual mice were labeled with one of the following antibodies before pooling in order to identify cells from individual tumors in downstream analysis: 1) TCR (TotalSeq™-C0120 anti-mouse TCR β chain antibody, Cat# 109259, BioLegend), 2) CD90.2 (TotalSeq™-C0075 anti-mouse CD90.2 (Thy1.2) antibody, Cat#, 105353, BioLegend), and 3) CD45 (TotalSeq™-C0096 anti-mouse CD45 antibody, Cat# 103169, BioLegend). Samples were submitted to the Genome Institute at Washington University in St. Louis to generate 10x libraries using 10x 5'v2 Single Cell RNAseq, V(D)J enrichment, feature barcoding, and Barcode Enabled Antigen Mapping kits. Fastq files were processed using the Cell Ranger (v7.1.0) multi pipeline with the default parameters. Gene expression libraries were aligned to the mouse transcriptome (mm10-2020-A) and TCR sequences were aligned to the VDJ reference dataset (GRCm38-alts-ensembl-5.0.0).
 
Contributor(s) Kumar M, Moynihan K, Sultan H, Schreiber R, Yeung YA, Djuretic I
Citation(s) 38563906
BioProject PRJNA1049835
Submission date Jan 05, 2024
Last update date Jul 02, 2024
Contact name Manu Kumar
E-mail(s) mkumar@asherbio.com
Organization name Asher Biotherapeutics
Street address 650 Gateway Blvd Suite 100
City South San Francisco
State/province California
ZIP/Postal code 94080-7014
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (58)
GSM8004779 Veh_D2_GEX
GSM8004780 aPD1_D2_GEX
GSM8004781 naIL2_D2_GEX

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
GSE252650_processed_data_files.tar.gz 682.4 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA

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