Systems and methods for determining nucleic acids

Abstract

The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.

1 - 176 . (canceled) 
     
     
         177 . A composition, comprising:
 a plurality of nucleic acid probes, each comprising a first portion comprising a target sequence and a plurality of read sequences, wherein the plurality of read sequences are distributed on the plurality of nucleic acid probes so as to define an error-correcting code.   
     
     
         178 . The composition of  claim 177 , wherein the plurality of nucleic acid probes defines a code space with a Hamming distance of at least 2 or at least 3. 
     
     
         179 . The composition of  claim 178 , wherein the code is a Hamming(7, 4) code 
     
     
         180 . The composition of  claim 178 , wherein the code is a Hamming(15, 11) code. 
     
     
         181 . The composition of  claim 178 , wherein the code is a Hamming(31, 26) code. 
     
     
         182 . The composition of  claim 178 , wherein the code is a Hamming(63, 57) code. 
     
     
         183 . The composition of  claim 178 , wherein the code is a Hamming(127, 120) code. 
     
     
         184 . The composition of  claim 177 , wherein the code is a SECDED code. 
     
     
         185 . The composition of  claim 184 , wherein the code is a SECDED (8, 4) code 
     
     
         186 . The composition of  claim 184 , wherein the code is a SECDED (16, 4) code. 
     
     
         187 . The composition of  claim 184 , wherein the code is a SECDED (16, 11) code. 
     
     
         188 . The composition of  claim 184 , wherein the code is a SECDED (22, 16) code. 
     
     
         189 . The composition of  claim 184 , wherein the code is a SECDED (39, 32) code. 
     
     
         190 . The composition of  claim 184 , wherein the code is a SECDED (72, 64) code. 
     
     
         191 . The composition of  claim 177 , wherein the code is a MHD4 code or a MHD2 code. 
     
     
         192 . The composition of  claim 177 , wherein the plurality of nucleic acid probes comprises no more than 100, no more than 64, no more than 32, no more than 16, or no more than 8, no more than 6, no more than 4, or no more than 2 possible read sequences. 
     
     
         193 . The composition of  claim 177 , wherein:
 (a) the target sequence of the plurality of nucleic acid probes has an average length of between 10 and 200 nucleotides;   (b) the plurality of read sequences have an average length of between 5 nucleotides and 50 nucleotides;   (c) the plurality of nucleic acid probes have an average length of between 10 and 300 nucleotides; or   (d) combinations of one or more of (a)-(c).   
     
     
         194 . The composition of  claim 177 , wherein at least some of the plurality of nucleic acid probes comprise DNA, RNA, PNA, LNA, or combinations thereof.