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Alternative transcript isoform detection with single cell and spatial resolution

Combining long sequencing reads with single cell assays enables the unambiguous identification of alternative splicing at single cell resolution. Traditional single cell assays have relied on short-read sequencing, which loses valuable information about transcript isoforms relevant to health, development, and disease.

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Alternative transcript isoforms have a range of implications in development, health, and disease. Studying alternative splicing and transcript isoforms, however, has been challenging for several reasons. One such difficulty is the common use of bulk sequencing, which only provides an average of the transcripts expressed across a population of cells. Another limitation has been the use of short-read sequencing methods, which lose key information from full-length transcripts. To unambiguously identify which isoforms are expressed, entire transcripts must be sequenced intact.

Current single cell gene expression library preparation methods fragment the cDNA to be compatible with shortread sequencers. These technologies also tend to bias captured transcripts to either the 5’ or 3’ ends. However, by combining single cell assays with long sequencing reads, it is now possible to identify alternative transcript isoforms with single cell resolution.

Genomics single cell