Whole transcriptome analysis in single cells

A method of detecting a plurality of target nucleic acids in a plurality of cells, the method comprising

• a. contacting the plurality of cells in a sample with an oligonucleotide primer for each target nucleic acid in the presence of a nucleic acid polymerase having a terminal transferase activity and extending the oligonucleotide primer to form a copy strand having one or more non-templated nucleotides at the 3′-end of the copy strand;
• b. for each target nucleic acid in each cell of the plurality of cells, forming a cell-characteristic compound barcode on the copy strand by sequentially attaching a series of barcode subunits to the 3′-end of the first copy strand by a split-pool process comprising one or more rounds of:
• i. distributing the sample into a first set of reaction volumes, each volume containing a first barcode subunit and a nucleic acid polymerase to extend the 3′-end of the copy strand to copy the first barcode subunit;
• ii. combining the first set of reaction volumes into a pool;
• iii. distributing the pool into a second set of reaction volumes, each volume containing a second barcode subunit and a nucleic acid polymerase to further extend the 3′-end of the copy strand to copy the second barcode subunit;
• c. determining the sequence of the extended copy strands including the cell-characteristic compound barcodes, thereby detecting the plurality of target nucleic acids in the plurality of cells.