Methods and compositions for tagging and analyzing samples

A method comprising:

• (a) providing a plurality of beads comprising a first plurality of DNA oligonucleotides;
• (b) providing a second plurality of DNA oligonucleotides, in which each DNA oligonucleotide of the second plurality comprises a promoter sequence, an adaptor sequence, a cell-tag, and a universal sequence;
• (c) merging the beads of (a) and the oligonucleotides of (b) into a first plurality of compartments such that each compartment of the first plurality of compartments comprises a single bead, a single DNA oligonucleotide of the second plurality of DNA oligonucleotides, primers, an RNA polymerase, and ribonucleotide triphosphates;
• (d) performing an amplification reaction on the DNA oligonucleotides within each compartment of the first plurality of compartments, thereby obtaining a third plurality of DNA oligonucleotides, in which each DNA oligonucleotide of the third plurality comprises the promoter sequence, the adaptor sequence, the cell tag, and the universal sequence;
• (e) performing an in vitro transcription reaction on the third plurality of DNA oligonucleotides within each compartment of the first plurality of compartments, thereby producing a plurality of RNA oligonucleotides comprising the adaptor sequence, the cell tag, and the universal sequence;
• (f) merging an interior of a compartment of the first plurality of compartments comprising the plurality of RNA oligonucleotides with an interior of a compartment of a second plurality of compartments to produce a plurality of merged compartments, wherein the compartment of the second plurality of compartments comprises target oligonucleotides from a single cell;
• (g) hybridizing the plurality of RNA oligonucleotides to the target oligonucleotides;
• and
• (h) performing a reaction to attach a sequence corresponding to the plurality of RNA oligonucleotides to the target oligonucleotides.