Disclosed herein are methods for performing in situ sequencing of
RNA transcripts with non-uniform 5′ ends. During reverse transcription (RT) of
RNA transcripts, RT
enzyme is induced to “template-switch” to a separate
oligonucleotide provided as the template for the upstream flanking region. This flanking region is grafted onto the beginning of the cDNA, enabling padlock probe detection, rolling circle amplification, and fluorescent in situ sequencing. Overall, the disclosed method for in situ sequencing can be applicable for analyzing exogenously introduced transcripts (e.g., identifying and determining
impact of a perturbation including a
CRISPR perturbation or shRNA / siRNA / ASO perturbation), analyzing naturally occurring transcripts (e.g., measuring
gene expression, detecting splicing events), and analyzing modified, naturally occurring transcripts (e.g., detecting mutations or
gene edits).