Provided are high throughput methods for physically linking cDNA molecules derived from mRNA molecules expressed by the same cell, and libraries of linked cDNA molecules produced by the methods. The methods comprise reverse transcribing mRNA from a single cell in a first container to produce cDNA molecules, and linking the cDNA molecules in a second container. The methods unexpectedly produced libraries of cDNA molecules with an increase in the number of molecules that are correctly linked to other molecules derived from the same cell.

Methods for CRISPR Enabled DNA Synthesis and compositions arising from the methods are provided. The methods may include ligation of partially single stranded DNA donor and acceptor oligonucleotides that are covalently linked to a subsequence of the target DNA to be sequenced followed by cleavage of the ligated product. In this manner the donor and acceptor oligonucleotides shuttle a growing subsequence of the target DNA with each cycle. A mutant Cpfl nuclease is missing non-specific ssDNA nuclease activity may be used for cleavage of the ligation product. Fourteen ligation/cleavage cycles can result in synthesis of ssDNA of greater than 10,000 bp in length.

Methods for CRISPR Enabled DNA Synthesis and compositions arising from the methods are provided. The methods may include ligation of partially single stranded DNA donor and acceptor oligonucleotides that are covalently linked to a subsequence of the target DNA to be sequenced followed by cleavage of the ligated product. In this manner the donor and acceptor oligonucleotides shuttle a growing subsequence of the target DNA with each cycle. A mutant Cpfl nuclease is missing non-specific ssDNA nuclease activity may be used for cleavage of the ligation product. Fourteen ligation/cleavage cycles can result in synthesis of ssDNA of greater than 10,000 bp in length.

Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.

Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.

The present invention concerns an oligonucleotide-functionalized hydrophobic polymer nanoparticle and method of its preparation. Said nanoparticle is a dye-loaded polymeric nanoparticle, and being functionalized by: (a) target-specific oligonucleotides, and/or (b) non-specific oligonucleotides.

The present invention concerns an oligonucleotide-functionalized hydrophobic polymer nanoparticle and method of its preparation. Said nanoparticle is a dye-loaded polymeric nanoparticle, and being functionalized by: (a) target-specific oligonucleotides, and/or (b) non-specific oligonucleotides.

The present invention concerns a method of sequencing immobilized polynucleotides in which beads which are tethered to the solid support are used as labels to identify bases within the polynucleotides. The beads carry sets of probes or bases which can bind to the polynucleotide allowing identification of the target base(s). Identification of the base(s) is achieved through sequential application of different cleavage means specific to different probes/bases carried on the beads. Also provided is an apparatus for performing the method and a kit comprising the apparatus and other components necessary for performing the method.

The present invention concerns a method of sequencing immobilized polynucleotides in which beads which are tethered to the solid support are used as labels to identify bases within the polynucleotides. The beads carry sets of probes or bases which can bind to the polynucleotide allowing identification of the target base(s). Identification of the base(s) is achieved through sequential application of different cleavage means specific to different probes/bases carried on the beads. Also provided is an apparatus for performing the method and a kit comprising the apparatus and other components necessary for performing the method.

The invention(s) cover a composition, where units of the composition are configured to interact with each other (e.g., as neighbors) in order enable decoding of positions of captured target material relative to neighboring units of the composition. In embodiments, the composition includes: a body; and a set of molecules coupled to the body, the set of molecules comprising a first subset and a second subset, wherein the first subset is structured for target analyte capture, and wherein the second subset is structured for interactions with one or more neighboring objects. The invention(s) also cover systems incorporating one or more units of the composition and methods implementing units of the composition.