The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.

中文翻译：

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使用 LR-Split-seq 以单细胞分辨率绘制差异 RNA 异构体表达的基因组基础并进行建模


长读长测序通量和质量的提高应该可以明确识别全长转录本亚型。然而，其在单细胞 RNA-seq 中的应用受到通量和费用的限制。在这里，我们开发并表征了长读段分割序列（LR-Split-seq），它使用组合条形码对具有长读段的单个细胞进行测序。应用于 C2C12 生肌系统时，LR-split-seq 将异构体与细胞类型相关联，具有相对经济性和设计灵活性。我们发现了分化过程中异构体表达变化的广泛证据，包括替代转录起始位点（TSS）和/或替代内外显子使用。 LR-Split-seq 提供了一种经济实惠的方法来识别单细胞中的簇特异性亚型。