Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq.
Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq.
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利用LR - Split - seq在单细胞分辨率下对差异RNA异构体表达的基因组基础进行定位和建模
DOI：
10.1186/s13059-021-02505-w
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发表时间：
2021-10-07
期刊：
影响因子：
12.3
通讯作者：
Mortazavi A
中科院分区：
文献类型：
--
作者：
Rebboah E;Reese F;Williams K;Balderrama-Gutierrez G;McGill C;Trout D;Rodriguez I;Liang H;Wold BJ;Mortazavi A
长读长测序通量和质量的提高应能明确鉴定全长转录异构体。然而，其在单细胞RNA测序中的应用受到通量和成本的限制。在此，我们开发并描述了长读长Split - seq（LR - Split - seq）技术，该技术利用组合条形码对单细胞进行长读长测序。将其应用于C2C12成肌系统时，LR - Split - seq以相对经济且设计灵活的方式将异构体与细胞类型相关联。我们发现了在分化过程中异构体表达变化的广泛证据，包括可变转录起始位点（TSS）和/或可变内部外显子使用情况。LR - Split - seq为鉴定单细胞中簇特异性异构体提供了一种经济实惠的方法。
网络版包含补充材料，可在10.1186/s13059 - 021 - 02505 - w获取。
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. The online version contains supplementary material available at 10.1186/s13059-021-02505-w.
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