Methods and compositions for tagging and analyzing samples

A method of tagging target oligonucleotides comprising:

• a. partitioning DNA into a plurality of compartments, wherein the DNA comprises an RNA polymerase promoter sequence, a tag sequence and a hybridization region capable of hybridizing to one or more target oligonucleotides, and wherein the plurality of compartments or a subset thereof further comprises an RNA polymerase and ribonucleotide triphosphates;
• b. performing an in vitro transcription reaction on the DNA within the compartments, thereby obtaining compartments comprising RNA, wherein the RNA comprises the tag sequence and the hybridization region;
• c. merging the interior of the compartments comprising RNA with the interior of a set of compartments comprising target oligonucleotides, wherein prior to the merging, the compartments comprising target oligonucleotides are physically separate from the compartments comprising RNA;
• d. hybridizing the RNA to the target oligonucleotides, wherein the hybridization region of the RNA hybridizes to a region of the target oligonucleotides;
• and
• e. performing a reaction to attach a sequence corresponding to the RNA to the target oligonucleotides, thereby tagging the target oligonucleotides.