GSM9238725: geo_submission_scRNAseq; Homo sapiens; RNA-Seq
For each sample, two formalin-fixed paraffin-embedded (FFPE) curls (25 μm each) were dissociated using the Miltenyi Biotech FFPE Tissue Dissociation Kit (CG000632 RevA, 10X Genomics). The resulting cell suspension was divided equally into four centrifuge tubes, each containing approximately 300,000 cells. Cells in each tube were hybridized with a unique Probe Barcode, as per the instructions in the "Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples" user guide (CG000527, 10X Genomics). Post-hybridization, cells from the four tubes were washed, counted, and pooled in equal proportions. Approximately 40,000 cells from the pooled suspension were loaded onto a Chromium Q chip (PN-1000422, 10X Genomics). Sequencing libraries were prepared and sequenced on an Illumina NovaSeq platform using paired-end dual-indexing (49 cycles for Read 1, 10 cycles for i7, 10 cycles for i5, and 90 cycles for Read 2). The sequencing data was demultiplexed using bcl2fastq (Illumina). The resulting FASTQ files were processed with Cell Ranger v7.0.1 (10X Genomics) using the multi pipeline and the GRCh38-2020-A reference genome. "Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples" user guide (CG000527, 10X Genomics)