Methods and systems for associating physical and genetic properties of biological particles

Abstract

Provided herein are methods and systems for processing a nucleic acid molecule from a biological particle (e.g., cell). A plurality of partitions (e.g., droplets) may be generated such that partitions of the plurality of partitions each include a biological particle (e.g., cell) comprising the nucleic acid molecule and a particle (e.g., bead). The partitions can be processed (e.g., imaged) to obtain one or more physical and/or optical properties of their respective biological particles. The nucleic acid molecules included in the partitions can be barcoded and sequenced (e.g., using nucleic acid barcode molecules coupled to the particles of the partitions) to generate nucleic acid sequences of the nucleic acid molecules. The nucleic acid sequences can be electronically associated with the one or more optical properties of the biological particles.

1 - 86 . (canceled) 
     
     
         87 . A method for analyzing a nucleic acid molecule of a cell, comprising:
 (a) partitioning into a physical partition of a plurality of physical partitions:
 (i) a bead comprising (I) an optical barcode and (II) a plurality of nucleic acid barcode molecules, wherein a nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules comprises a barcode sequence, and 
 (ii) said cell; 
   (b) generating (i) data corresponding to said optical barcode of said bead and (ii) data corresponding to a phenotypic property of said cell; and   (c) using said nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules and said nucleic acid molecule of said cell to conduct a barcoding reaction on said nucleic acid molecule to generate a barcoded nucleic acid molecule.   
     
     
         88 . The method of  claim 87 , further comprising associating said data corresponding to said optical barcode with said data corresponding to said phenotypic property of said cell. 
     
     
         89 . The method of  claim 87 , further comprising, associating said plurality of nucleic acid barcode molecules with said optical barcode. 
     
     
         90 . The method of  claim 87 , further comprising, determining a sequence of the barcoded nucleic acid molecule or derivative thereof. 
     
     
         91 . The method of  claim 90 , further comprising associating said determined sequence with said data corresponding to said optical barcode of said bead and said phenotypic property of said cell. 
     
     
         92 . The method of  claim 87 , wherein said cell is a live cell. 
     
     
         93 . The method of  claim 87 , wherein (b) comprises imaging said bead and said cell in said physical partition. 
     
     
         94 . The method of  claim 93 , wherein said imaging comprises bright field microscopy, fluorescence microscopy, phase contrast microscopy, multispectral microscopy, or polarization microscopy. 
     
     
         95 . The method of  claim 87 , wherein nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules comprise a common barcode sequence. 
     
     
         96 . The method of  claim 87 , wherein (b) and/or (c) is performed when said bead and said cell or macromolecular constituents of said cell are in said physical partition. 
     
     
         97 . The method of  claim 87 , wherein said plurality of physical partitions is a plurality of wells. 
     
     
         98 . The method of  claim 87 , wherein said plurality of physical partitions is a plurality of droplets. 
     
     
         99 . The method of  claim 87 , wherein said phenotypic property of said cell comprises one or more members selected from the group consisting of: a size, a shape, a surface marker on said cell, an inclusion in said cell, a structure of an organelle in said cell, a number of organelles in said cell, a secretion or excretion with respect to said cell, and a localization of an organelle in said cell. 
     
     
         100 . The method of  claim 87 , wherein said optical barcode has an associated optical intensity or frequency that is distinct among a plurality of additional optical barcodes partitioned in other physical partitions of said plurality of physical partitions. 
     
     
         101 . The method of  claim 87 , wherein said plurality of nucleic acid barcode molecules of said bead comprise said optical barcode. 
     
     
         102 . The method of  claim 87 , wherein said bead is a gel bead. 
     
     
         103 . The method of  claim 87 , wherein said plurality of nucleic acid barcode molecules is releasably coupled to said bead. 
     
     
         104 . The method of  claim 87 , further comprising, generating data corresponding to an identity of a protein of said cell. 
     
     
         105 . The method of  claim 104 , further comprising, associating said data corresponding to said identity of said protein with said data corresponding to said phenotypic property of said cell. 
     
     
         106 . The method of  claim 87 , wherein said optical barcode of said bead in said physical partition and an additional optical barcode of an additional bead in an additional physical partition of said plurality of physical partitions fluoresce at different wavelengths. 
     
     
         107 . The method of  claim 87 , wherein (a)-(c) are repeated for an additional physical partition of said plurality of physical partitions, wherein said additional physical partition comprises (i) an additional bead comprising an additional optical barcode and an additional plurality of nucleic acid barcode molecules, wherein an additional nucleic acid barcode molecule of said additional plurality of nucleic acid barcode molecules comprises an additional barcode sequence different than said barcode sequence and (ii) an additional cell comprising an additional nucleic acid molecule, and wherein said optical barcode of said bead in said physical partition and said additional optical barcode of said additional bead in said additional physical partition are different.