Methods for processing nucleic acid molecules

Abstract

The present disclosure provides methods, systems, and kits for processing nucleic acid molecules. A method may comprise providing a template nucleic acid fragment (e.g., within a cell, cell bead, or cell nucleus) within a partition (e.g., a droplet or well) and subjecting the template nucleic acid fragment to one or more processes including a barcoding process and a single primer extension or amplification process. The processed template nucleic acid fragment may then be recovered from the partition and subjected to further amplification to provide material for subsequent sequencing analysis. The methods provided herein may permit simultaneous processing and analysis of both DNA and RNA molecules originating from the same cell, cell bead, or cell nucleus.

1 .- 30 . (canceled) 
     
     
         31 . A method for processing a nucleic acid sample, comprising:
 a) providing a biological particle comprising a deoxyribonucleic acid (DNA) molecule and a ribonucleic acid (RNA) molecule within a partition among a plurality of partitions, wherein said partition comprises a first nucleic acid barcode molecule and a second nucleic acid barcode molecule, wherein said first nucleic acid barcode molecule and said second nucleic acid barcode molecule comprise a common barcode sequence;   b) within said partition, generating (i) a first barcoded nucleic acid product from said DNA molecule and said first nucleic acid barcode molecule and (ii) a second barcoded nucleic acid product from said RNA molecule and said second nucleic acid barcode molecule, wherein said first barcoded nucleic acid product and said second barcoded nucleic acid product comprise said common barcode sequence, or a complement thereof;   c) recovering said first barcoded nucleic acid product and said second barcoded nucleic acid product from said partition;   d) processing said first barcoded nucleic acid product to generate a processed nucleic acid product comprising a dA tail; and   e) using (i) said processed nucleic acid product to generate a first plurality of amplification products and (ii) said second barcoded nucleic acid product to generate a second plurality of amplification products.