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 for providing a composition comprising a plurality of droplets comprising nucleic acid sequence adapters comprising an identification sequence and a restriction site, comprising:
 providing the adapters on a solid support binding the adapters to nucleic acids;   producing droplets in a microfluidic device, the device comprising at least two microfluidic channels combined via a junction, wherein the fluid forming the droplets is substantially immiscible with the carrier fluid surrounding the droplets; and   encapsulating the adapters, the nucleic acids and the solid support in at least some of the droplets.   
     
     
         113 . The method of  claim 112 , wherein the junction is selected from the group consisting of a T-junction, a Y-junction, a channel-within-a-channel junction, a cross junction, and a flow-focus junction. 
     
     
         114 . The method of  claim 112 , wherein the adapters comprise primer sites. 
     
     
         115 . The method of  claim 114 , wherein the primer sites comprise a universal primer. 
     
     
         116 . The method of  claim 112 , wherein the solid support is a bead. 
     
     
         117 . The method of  claim 112 , wherein the nucleic acids are RNA. 
     
     
         118 . The method of  claim 112 , wherein the nucleic acids are DNA. 
     
     
         119 . The method of  claim 112 , wherein the adapters further comprise a sequence recognizable by a primer, wherein the identification sequence comprises a barcode, and wherein the restriction is cleavable by a restriction endonuclease. 
     
     
         120 . The method of  claim 112 , wherein the identification sequences provide a unique identifier for each individual cell.