Single cell isoform profiling, 10xGenomics scRNA-seq and nanopore long read sequencing
About Kevin Lebrigand
Kevin Lebrigand is Head of Bioinformatics at UCAGenomiX, the functional genomics platform of Nice-Sophia-Antipolis, one of the core nodes of the "France Genomique" network, using next generation sequencing to perform a broad range of sequencing projects such as de novo genome assembly, RNA-seq, small RNA-seq, CHIP-seq and CLIP-seq. In 2014 the platform decided to focus their expertise on methodological developments around single cell transcriptomics using the Fluidigm C1, and more recently the 10xGenomics Chromium system, on which more than 120 samples has been profiled. Last summer Kevin acquired a PromethION long-read sequencer to perform isoform-level profiling at the single cell level.
Single cell transcriptome sequencing has become a powerful tool for high-resolution analysis of gene expression in individual cells. However, current high throughput approaches only allow sequencing of one extremity of the transcript (transcriptome profiling). Information crucial for an in-depth understanding of cell-to-cell heterogeneity on splicing, chimeric transcripts and sequence diversity (SNPs, RNA editing, imprinting) is lost. Here we present an approach that uses Oxford Nanopore sequencing with unique molecular identifiers to obtain error corrected full length single cell sequence information with the 10xGenomics single cell isolation system and apply it to examine differential RNA alternative splicing and RNA editing events in the embryonic mouse brain.