The invention is directed to modified oligonucleotide compositions and methods for selectively reducing unwanted nucleic acid contaminants and enriching for desired nucleic acid targets from complex genomic nucleic acid mixtures for sequencing applications. The modified oligonucleotide compositions include one or more modified groups that increase the T.sub.m of the resultant oligonucleotide composition.

The invention is directed to modified oligonucleotide compositions and methods for selectively reducing unwanted nucleic acid contaminants and enriching for desired nucleic acid targets from complex genomic nucleic acid mixtures for sequencing applications. The modified oligonucleotide compositions include one or more modified groups that increase the T.sub.m of the resultant oligonucleotide composition.

Described herein are methods of preparing dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing. In various embodiments, the methods use a two-step indexing process to tag bisulfite-treated DNA with unique molecular identifiers (UMIs).

Described herein are methods of preparing dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing. In various embodiments, the methods use a two-step indexing process to tag bisulfite-treated DNA with unique molecular identifiers (UMIs).

A DNA nanoarray includes a milliscale chip substrate; a microscale binder spot having a uniform surface bound to the substrate; and immobilized oligonucleotide sequences, each linked to the binder. The immobilized oligonucleotide sequences form a monolayer, each having a length that guarantees within a statistical certainty that the immobilized oligonucleotide sequences are each unique. A method of producing the DNA nanoarray includes providing a streptavidin-coated substrate; patterning the substrate by photolithography; and immobilizing biotin-tagged oligonucleotides on the patterned surface. The oligonucleotides each have a unique string of bases. The patterned surface has an array of microscale spots with active streptavidin binding sites. Immobilization includes applying a solution containing the oligonucleotides to the microscale spots; applying a buffer over the patterned surface; and washing the patterned surface in buffered saline solution. Bits and/or spatial patterns may be stored the DNA nanoarray, then read and/or visualized.

A DNA nanoarray includes a milliscale chip substrate; a microscale binder spot having a uniform surface bound to the substrate; and immobilized oligonucleotide sequences, each linked to the binder. The immobilized oligonucleotide sequences form a monolayer, each having a length that guarantees within a statistical certainty that the immobilized oligonucleotide sequences are each unique. A method of producing the DNA nanoarray includes providing a streptavidin-coated substrate; patterning the substrate by photolithography; and immobilizing biotin-tagged oligonucleotides on the patterned surface. The oligonucleotides each have a unique string of bases. The patterned surface has an array of microscale spots with active streptavidin binding sites. Immobilization includes applying a solution containing the oligonucleotides to the microscale spots; applying a buffer over the patterned surface; and washing the patterned surface in buffered saline solution. Bits and/or spatial patterns may be stored the DNA nanoarray, then read and/or visualized.

The present disclosure relates to materials and methods for spatial detection of nucleic acid in a tissue sample or a portion thereof. In particular, provided herein are materials and methods for detecting RNA so as to obtain spatial information about the localization, distribution or expression of genes in a tissue sample. In some embodiments, the materials and methods provided herein enable detection of gene expression in a single cell.

The present disclosure relates to materials and methods for spatial detection of nucleic acid in a tissue sample or a portion thereof. In particular, provided herein are materials and methods for detecting RNA so as to obtain spatial information about the localization, distribution or expression of genes in a tissue sample. In some embodiments, the materials and methods provided herein enable detection of gene expression in a single cell.

There is described herein, a method of capturing and analyzing cell-free methylated DNA in a sample. The method involves subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA. A predetermined amount of control synthetic DNA fragments are added to the sample. The control synthetic DNA fragments each have a known nucleic acid sequence that does not align to a target genome sequence, and at least some of the control synthetic DNA fragments are methylated. The sample is denatured, and cell-free methylated DNA and the control synthetic DNA fragments are captured using a binder selective for methylated polynucleotides. The captured DNA is amplified and sequenced.

Provided herein are modified Archaeal family B polymerases derived from the Archaeal microorganism Thermococcus sp. EP1 that exhibit improved incorporation of nucleotide analogues utilized in DNA sequences.