GSM5984967: scRNA data for RCC Chromophobe patient presented in Fig. 1; Homo sapiens; RNA-Seq
Tumor samples were directly obtained from the operating room during nephrectomy.  Tissue samples were placed in separate labeled containers containing Roswell Park Memorial Institute (RPMI) medium and transported in regular ice to the laboratory. The CPTs were transported at room temperature. Overall transit time in all cases was less than 1 hour (from specimen extraction to cell dissociation) and the tissue samples were always kept in this medium. The chRCC patient was an 84-year-old female with stage III disease and was treatment-naïve at the time of sample collection. RNA libraries were prepared for sequencing using standard Illumina protocols.  A suspension of 10,000 FACS sorted live cells in 1X PBS (calcium and magnesium free) containing 0.04% BSA (Sigma) were used as input to the 10X chromium controller system (10x Genomics Inc., product code 120223). Cells were barcoded using the 10x™ GemCode™ Technology to separately index each cell's transcriptome by partitioning them into Gel Bead-in-EMulsions (GEMs). GEMs were generated by combining barcoded Single Cell 5' Gel Beads, RT Master Mix with cells, and Partitioning Oil on a microfluidic chip. The GEM RT reaction was performed in thermocycler (53°C for 45 minutes, 85°C for 5 minutes, 4°C hold overnight). After RT incubation, the GEMs were broken, and the first strand of cDNA was recovered using DynaBeadsR MyOne™ Silane beads. 2 – 50 ng of amplified cDNA and the target enriched product respectively were used as input for library construction. Fragmentation, end repair and A tailing were performed to obtain final libraries containing the P5 and P7 priming sites used in IlluminaR sequencing. High sensitivity DNA chips and the Agilent 2100 bioanalyzer (Agilent Technologies) were used for 5' gene expression quality control and quantification. Quality control was performed twice before sequencing. The 5' gene expression library was sequenced on NovaSeq 6000 S1 with sequencing depth of approximately 300-500 million reads per sample. For the mouse dataset, live, CD45+CD3-NK1.1+ innate lymphocytes from the pooled tumors of one PyMT mouse were sorted into 1X PBS containing 0.04% BSA. Library preparation, quality control and single-cell RNA sequencing were performed by the Integrated Genomics Operations Core of Sloan Kettering Institute at MSKCC.