Methods and kits for labeling cellular molecules

A method of cell-specifically labeling RNA molecules within cells, the method comprising:

• (a) fixing and permeabilizing a plurality of cells;
• (b) generating complementary DNA (cDNA) molecules within the plurality of cells by reverse transcribing RNA molecules within the cells, wherein the RNA molecules are reverse transcribed using reverse transcription (RT) primers each comprising:
• a poly(T) sequence or a random nucleotide sequence, and
• a 5′ overhang comprising a 5′ overhang sequence;
• and
• (c) tagging the cDNA molecules with one or more barcode sequences by performing steps (i) through (iii) one or more times:
• (i) dividing the plurality of cells comprising the cDNA molecules into a plurality of aliquots, wherein each aliquot comprises more than one cell;
• (ii) coupling nucleic acid tags to cDNA molecules within cells of the aliquots, wherein each nucleic acid tag comprises a barcode sequence, and wherein the barcode sequences present within the nucleic acid tags are specific to each aliquot;
• and
• (iii) combining the cells from the plurality of aliquots.