Project description:Frozen PBMC samples containing at least 1 million cells were thawed for 1 minute at 37C and washed twice with RPMI complete media (10% FBS with glutamate and Pen/Strep). All of the samples had >80% viable cells. Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library and Gel bead kit v2 (PN-120237) following manufacturer’s user guide (CG00052, 10x Genomics, Pleasanton, CA). The total cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~ 6,000 cells per sample. cDNAs and libraries were prepared following manufacturer’s user guide (10x Genomics). cDNA amplification and indexed libraries were prepared using 12 and 14 cycles of PCR, respectively. Libraries were profiled, quantified, and sequenced as 5’ single-cell gene expression libraries.

| EGAS00001004008 | EGA

Single cell RNAseq of PBMC from bladder cancer patients

Project description:Frozen PBMC samples containing at least 1 million cells were thawed for 1 minute at 37Ã¯Â‚Â°C and washed twice with RPMI complete media (10% FBS with glutamate and Pen/Strep). All of the samples had >80% viable cells. Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3Ã¢Â€Â™ Library and Gel bead kit v2 (PN-120237) following manufacturerÃ¢Â€Â™s user guide (CG00052, 10x Genomics, Pleasanton, CA). The total cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~ 6,000 cells per sample. cDNAs and libraries were prepared following manufacturerÃ¢Â€Â™s user guide (10x Genomics). cDNA amplification and indexed libraries were prepared using 12 and 14 cycles of PCR, respectively. Libraries were profiled, quantified, and sequenced as 5Ã¢Â€Â™ single-cell gene expression libraries.

| EGAS00001004458 | EGA

A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity.

Project description: Not available

| S-EPMC10837414 | biostudies-literature

Evaluation of single-cell RNAseq labelling algorithms using cancer datasets.

Project description: Not available

| S-EPMC9851326 | biostudies-literature

Single cell RNAseq of PBMC from RCC patients

| EGAS00001004451 | EGA

Epigenetic priming induces cancer testis antigens and human endogenous retroviruses in glioma for enhanced T cell responses at single cell resolution (methylation)

Project description:Glioblastoma (GBM) is the most common malignant primary brain tumor and remains incurable. Previous work has shown that systemic administration of Decitabine (DAC) induces sufficient expression of NY-ESO-1 in GBM for targeting by adoptive T-cell therapy in vivo. However, the mechanisms by which DAC enhances immunogenicity in GBM remain to be elucidated. Using patient tissue, immortalized glioma cells, and primary patient-derived gliomaspheres, we demonstrate in vitro that basal NY-ESO-1 expression is restricted by promoter hypermethylation in gliomas. DAC treatment of glioma cells specifically inhibits DNA methylation silencing and renders NY-ESO-1 an inducible tumor antigen. Targeting of DAC-induced NY-ESO-1 in primary GBM cells promotes specific and polyfunctional NY-ESO-1 TCR-T cell responses. DAC further upregulates other tumor-associated cancer testis antigens concomitantly with tumor-intrinsic reactivation of human endogenous retroviruses (hERV) and type I interferon. Overall, we demonstrate that DAC promotes an inducible tumor antigen and enhances T cell functionality against GBM.

2024-06-04 | GSE261190 | GEO

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