Whole transcriptome analysis in single cells

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

• a. contacting each target nucleic acid of the plurality of target nucleic acids in the plurality of cells with an oligonucleotide primer, wherein the contacting is performed in the presence of a nucleic acid polymerase having a terminal transferase activity;
• b. extending the oligonucleotide primer to form a copy strand having one or more non-templated nucleotides at a 3′-end;
• c. for each target nucleic acid of the plurality of target nucleic acids in the plurality of cells, generating a cell-characteristic compound barcode on the copy strand by sequentially attaching a series of barcode subunits to the 3′-end of the 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 first reaction volume comprising 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 second reaction volume comprising 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;
• d. determining the sequence of the extended copy strands including the generated cell-characteristic compound barcodes, thereby detecting the plurality of target nucleic acids in the plurality of cells.