Systems and methods for epigenetic sequencing

Abstract

The present invention generally relates to microfluidics and/or epigenetic sequencing. In one set of embodiments, cells contained within a plurality of microfluidic droplets are lysed and the DNA (e.g., from nucleosomes) within the droplets are labeled, e.g., with adapters containing an identification sequence. The adapters may also contain other sequences, e.g., restriction sites, primer sites, etc., to assist with later analysis. After labeling with adapters, the DNA from the different cells may be combined and analyzed, e.g., to determine epigenetic information about the cells. For example, the DNA may be separated on the basis of certain modifications (e.g., methylation), and the DNA from the separated nucleosomes may be sequenced using techniques such as chromatin immunoprecipitation (“ChIP”). In some cases, the DNA sequences may also be aligned with genomes, e.g., to determine which portions of the genome were epigenetically modified, e.g., via methylation.

What is claimed is: 
     
         1 - 111 . (canceled) 
     
     
         112 . A method comprising:
 providing a solution comprising a plurality of nucleic acid sequences originating from a plurality of cells, at least some of the nucleic acid sequences being attached to an adapter, the adapter comprising an identification sequence, wherein sequences originating from the same cell contain identical identification sequences, and sequences originating from different cells contain different identification sequences, the adapter further comprising a primer site and a cleavage site, which is cleavable by a restriction endonuclease, wherein the adapters are present on a solid support; and   amplifying at least some of the sequences.   
     
     
         113 . The method of  claim 112 , comprising cleaving the adapter at the cleavage site. 
     
     
         114 . The method of  claim 112 , wherein the solution is contained within a droplet. 
     
     
         115 . The method of  claim 112 , wherein the plurality of nucleic acid sequences comprises DNA. 
     
     
         116 . The method of  claim 112 , wherein the plurality of nucleic acid sequences comprises RNA. 
     
     
         117 . The method of  claim 116 , wherein the RNA molecules are barcoded or ligated with an identification sequence using adaptors. 
     
     
         118 . The method of  claim 112 , wherein the primer site comprises a universal primer. 
     
     
         119 . The method of  claim 112 , wherein the primer site comprises a PCR primer site. 
     
     
         120 . The method of  claim 112 , wherein the identification sequences are added to each droplet and added to the fragmented DNA sequences, providing a unique identifier for each individual cell. 
     
     
         121 . The method of  claim 112 , wherein the cleavage site is a restriction site cleavable by a restriction endonuclease. 
     
     
         122 . A method comprising:
 providing a solution comprising a plurality of nucleic acid sequences originating from a plurality of cells, at least some of the nucleic acid sequences being attached to an adapter, the adapter comprising an identification sequence, wherein sequences originating from the same cell contain identical identification sequences, and sequences originating from different cells contain different identification sequences; and   sequencing at least some of the sequences.