Methods for analyzing nucleic acids

Abstract

Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.

What is claimed: 
     
         1 . A method for biological analysis, the method comprising:
 (a) providing a plurality of polynucleotides derived from a tissue sample;   (b) generating a plurality of tagged polynucleotides from said plurality of polynucleotides and a plurality of oligonucleotide tags, wherein a tagged polynucleotide of the plurality of tagged polynucleotides comprises:
 (i) a first tag sequence corresponding to a site within said tissue sample; and 
 (ii) a second tag sequence distinguishing said tagged polynucleotide from other tagged polynucleotides of the plurality of tagged polynucleotides; 
   (c) sequencing said plurality of tagged polynucleotides to determine sequences corresponding to the plurality of polynucleotides, including the first tag sequence and the second tag sequence; and   (d) using the sequences determined in step (c) to count polynucleotides for multiple different polynucleotides derived from said tissue sample.