biostudies-arrayexpressDr Rupesh DashHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15148This study employs single-cell sequencing to identify rare, transient cisplatin-resistant subpopulations in OSCC, analyzing their gene expression and signaling pathways. By targeting these vulnerable cell states, we aim to develop combination therapies that prevent resistance emergence, enhancing cisplatin’s effectiveness and overcoming treatment failure in oral squamous cell carcinoma.biostudies-arrayexpressSequencing - Sequencing was performed on an Illumina NextSeq 500 using 300 bp paired-end reads with a target depth of 2000 reads per cell.Nucleic Acid Extraction - The single cell suspension was converted to single-cell gel beads in the emulsion (GEMs) by using the Chromium Single Cell 5′ Library and Gel Bead kit, and Chromium Single Cell G Chip kit (10x Genomics) according to the manufacturer’s protocolLibrary Construction - scRNA-seq libraries were constructed using a Single Cell 5′ Library and Gel Bead kit, according to manufacturer's protocol. The cells from SCC9 CIsS, SCC9 4MCisR, SCC9 8MCisR cell types which were tagged using TotalSeq™-C antibodies (C0251, C0252, C0253) respectively.Sample Collection - SCC9 CIsS, SCC9 4MCisR, SCC9 8MCisR cells were cultured in cell culture conditions in DMEM-F12 (10%FBS) . Cells were trypsinized and subjected to 10X genomics for GEM generation.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The hashtag samples were demultiplexed using the HTO demux pipeline. The three samples were normalised for cell counts using Sctransform method.Sequence Alignment - The Cell Ranger mkfastq (v5) from 10× Genomics was used to demultiplex raw BCL files to fastq files. The generated fastq files were then aligned to the human reference genome (refdata-cellranger-GRCh38-3.0.0) using cellranger multi. 10× feature barcode information was included in the feature reference. The resulting output generated was a gene expression matrix and feature barcode counts for each cell barcode. The matrix was then processed in R (v4.1) using the Seurat package (v4.3)UnknownTranscriptomicsGenomicsProteomicsNextSeq 550RNA-seq of coding RNA from single cellsHomo sapiensDr Rupesh DashfalseBASP1 drives cisplatin resistance through LIN7A mediated epithelial-mesenchymal transition in OSCC - single cell RNA seqThis study employs single-cell sequencing to identify rare, transient cisplatin-resistant subpopulations in OSCC, analyzing their gene expression and signaling pathways. By targeting these vulnerable cell states, we aim to develop combination therapies that prevent resistance emergence, enhancing cisplatin’s effectiveness and overcoming treatment failure in oral squamous cell carcinoma.2026-02-02T00:00:00Z2026-02-02T05:17:25.303Z2025-05-19T14:21:52.606ZE-MTAB-15148ERP172723EFO_0002944EFO_0004170EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184