Trans-splicing transcriptome profiling

A method of identifying mRNA transcripts in the transcriptomes of multiple cells within a population of cells comprising

• i) delivering into each of at least two cells a donor expression vector comprising nucleotides in a sequence encoding a trans-splicing barcode cassette, wherein the trans-splicing barcode cassette comprises
• a) a first portion, the nucleotide sequence of which encodes an intron comprising as part of its 3′ end, or followed at its 3′ end by a splice-site nucleotide sequence;
• followed at its 3′ end by,
• b) a second portion, the nucleotide sequence of which encodes a barcode polynucleotide;
• followed at its 3′ end by
• c) a third portion, which encodes a nucleotide identification element sequence,
• ii) exposing the cell to conditions such that each of the at least two cells produces multiple copies of the trans-splicing barcode cassette encoded by the donor expression vector, which multiple copies of the trans-splicing barcode cassette each splice the barcode polynucleotide onto a mRNA transcript of the at least two cells, thereby forming multiple spliced mRNA transcripts of the cell, each spliced to the barcode polynucleotide;
• and
• iii) identifying the multiple mRNA transcripts that are spliced to the barcode polynucleotides, thereby identifying mRNA transcripts in the transcriptomes of multiple cells within a population of cells.