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 having the same nucleotide sequence, 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,
• wherein the portion of the nucleotide sequence of the expression vector that encodes the barcode polynucleotide is altered within the at least two cells, such that each of the at least two cells within the population expresses copies of the trans-splicing barcode cassette having a unique barcode polynucleotide sequence,
• ii) exposing the cells 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.