Methods and compositions for barcoding nucleic acid libraries and cell populations

A method of generating a barcoded nucleic acid library, comprising:

• a. delivering one or more polynucleotides into a cell, each polynucleotide comprising:
• i. a sequence encoding a barcoding construct operably linked to a first promoter that is an antisense promoter, wherein the barcoding construct comprises a trans-splicing element and a barcode sequence;
• and
• ii. a sequence encoding a perturbation element operably linked to a second promoter;
• b. generating RNA transcripts of the one or more polynucleotides delivered into the cell, wherein the RNA transcripts comprise the barcoding construct and the perturbation element;
• and
• c. splicing the barcoding sequence onto endogenous RNA molecules in the cell, thereby generating a barcoded library, each member of the barcoded library comprising the barcode sequence and the endogenous RNA molecules attached with the barcode sequence.

A method of labeling cell populations, comprising:

• a. delivering a plurality of polynucleotides into a plurality of cell populations, each polynucleotide comprising a sequence encoding a barcoding construct operably linked to an antisense promoter, wherein the barcoding construct comprises a trans-splicing element and a barcode sequence;
• b. in each cell, generating RNA transcripts of the polynucleotides, wherein the transcripts comprise the barcoding constructs;
• and
• c. splicing each of the barcoding sequence onto endogenous RNA molecules in the cells, wherein cells in the same cell population comprise a common barcode sequence and the barcode sequence in each cell population is unique.

A method of performing whole-organism barcoding in a subject, comprising:

• a. delivering a plurality of polynucleotides into multiple types of cells in the subject, each polynucleotide comprising a sequence encoding a barcoding construct operably linked to an antisense promoter, wherein the barcoding construct comprises a trans-splicing element and a barcode sequence, and the antisense promoter is a cell-specific promoter;
• b. in each cell, generating RNA transcripts of the polynucleotides, wherein the transcripts comprise the barcoding constructs;
• and
• c. splicing each of the barcoding sequences onto endogenous RNA molecules in the cells, wherein cells in the same type of cells comprise a common barcode sequence and the barcode sequence in each type of cells is unique.