Studying the consequences of somatic mutations in pre-malignant and cancerous tissues is challenging due to noise in single-cell transcriptome data and difficulty in identifying the clonal identity of single cells. We optimized TARGET-seq to develop TARGET-seq+, which combines RNA sequencing (RNA-seq), the analysis of cell surface protein expression, and genotyping in single cells with improved sensitivity. We describe the steps for cell isolation, the preparation of single-cell RNA-seq (scRNA-seq) and genotyping libraries, and sequencing. We also provide guidance on the analysis of single-cell genotyping, transcriptome pre-processing, and data integration. For complete details on the use and execution of this protocol, please refer to Jakobsen et al.1.
Journal article
2025-06-20T00:00:00+00:00
6
Flow Cytometry, Gene Expression, Genomics, Molecular Biology, RNA-seq, Sequencing, Single Cell, Stem Cells, Single-Cell Analysis, Membrane Proteins, Humans, Sequence Analysis, RNA, Genotyping Techniques, RNA-Seq, Genotype, High-Throughput Nucleotide Sequencing