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