In various embodiments, the invention teaches methods for detecting ribonucleic acid (RNA) molecules that contain certain chemical modifications using sequencing technologies. These modified RNAs are otherwise not readily detected using the commonly used cloning protocols required for sequencing. The method further includes bioinformatics analyses to identify specific RNA species that are modified at high resolution.

In various embodiments, the invention teaches methods for detecting ribonucleic acid (RNA) molecules that contain certain chemical modifications using sequencing technologies. These modified RNAs are otherwise not readily detected using the commonly used cloning protocols required for sequencing. The method further includes bioinformatics analyses to identify specific RNA species that are modified at high resolution.

A method for producing a nucleic acid molecule from a template nucleic acid sequence and a linking unit attached to a primer, which method comprises a step of contacting the template nucleic acid sequence with a nucleic acid polymerase under conditions which allow the nucleic acid polymerase to produce the nucleic acid molecule from the primer based on the template nucleic acid sequence, wherein the linking unit is attached to a target site in the template nucleic acid sequence with a covalent linkage.

A method for producing a nucleic acid molecule from a template nucleic acid sequence and a linking unit attached to a primer, which method comprises a step of contacting the template nucleic acid sequence with a nucleic acid polymerase under conditions which allow the nucleic acid polymerase to produce the nucleic acid molecule from the primer based on the template nucleic acid sequence, wherein the linking unit is attached to a target site in the template nucleic acid sequence with a covalent linkage.

A method for the rapid and efficient production of guide strand libraries such as CRISPR gRNA libraries is disclosed.

A method for the rapid and efficient production of guide strand libraries such as CRISPR gRNA libraries is disclosed.

Methods for constructing consecutively connected and optionally truncated copies of nucleic acid molecules are disclosed. Consecutively connected copies of nucleic acid molecules can be used to perform sequencing of the same nucleic acid molecules several times, improving overall accuracy of sequencing. Sequencing of truncated copies of nucleic acid molecules can be used to deduce the sequences of nucleic acid molecules from assembling short sequenced segments. Connected copies of nucleic acid molecules can be constructed by first attaching hairpin adaptors to the nucleic acid molecules, and then using strand displacing polymerases to generate complementary strands of the nucleic acid molecule strands connected by the hairpin adaptors.

Methods for constructing consecutively connected and optionally truncated copies of nucleic acid molecules are disclosed. Consecutively connected copies of nucleic acid molecules can be used to perform sequencing of the same nucleic acid molecules several times, improving overall accuracy of sequencing. Sequencing of truncated copies of nucleic acid molecules can be used to deduce the sequences of nucleic acid molecules from assembling short sequenced segments. Connected copies of nucleic acid molecules can be constructed by first attaching hairpin adaptors to the nucleic acid molecules, and then using strand displacing polymerases to generate complementary strands of the nucleic acid molecule strands connected by the hairpin adaptors.

Filtering small nucleic acids using permeabilized cells and methods for using the filtering to detect genomic DNA accessibility are described.

Filtering small nucleic acids using permeabilized cells and methods for using the filtering to detect genomic DNA accessibility are described.