This disclosure demonstrates an approach that translates synthetic DNA codes to spatial codes registered in nanoliter microchambers for multiplexed measurement of nearly any type of molecular targets (e.g., miRNAs, mRNAs, intracellular and surface proteins) in single cells.

In one embodiment, provided are a method for analyzing at least one nucleic acid that can conveniently and highly accurately analyze even a very small number of analyte at least one nucleic acid. In one embodiment, the present invention relates to a method for analyzing at least one nucleic acid, comprising: a library preparation step of preparing a library comprising at least one standard nucleic acid of specific copy number(s) and at least one analyte nucleic acid in a same system; a calibration curve data generation step of generating calibration curve data based on the copy number(s) of the at least one standard nucleic acid of specific copy number(s); and an analyte nucleic acid analysis step of identifying at least one nucleotide sequence of the analyte nucleic acid while identifying the number(s) of the at least one nucleotide sequence of the at least one analyte nucleic acid using the calibration curve data.

In one embodiment, provided are a method for analyzing at least one nucleic acid that can conveniently and highly accurately analyze even a very small number of analyte at least one nucleic acid. In one embodiment, the present invention relates to a method for analyzing at least one nucleic acid, comprising: a library preparation step of preparing a library comprising at least one standard nucleic acid of specific copy number(s) and at least one analyte nucleic acid in a same system; a calibration curve data generation step of generating calibration curve data based on the copy number(s) of the at least one standard nucleic acid of specific copy number(s); and an analyte nucleic acid analysis step of identifying at least one nucleotide sequence of the analyte nucleic acid while identifying the number(s) of the at least one nucleotide sequence of the at least one analyte nucleic acid using the calibration curve data.

This document provides methods and materials related to genetic variations of neurological disorders. For example, this document provides methods for using such genetic variations to assess susceptibility of developing Parkinson's disease.

This document provides methods and materials related to genetic variations of neurological disorders. For example, this document provides methods for using such genetic variations to assess susceptibility of developing Parkinson's disease.

Methods and systems for highly sensitive detection of methylation changes in DNA samples are provided, particularly in DNA samples obtained from biological fluids such as plasma and urine.

Methods and systems for highly sensitive detection of methylation changes in DNA samples are provided, particularly in DNA samples obtained from biological fluids such as plasma and urine.

This specification discloses a novel methodology for labelling RNA via enzymatic incorporation of a minimally perturbing fluorescent tricyclic cytosine analogue. This analogue is shown to be 100% incorporated in example transcripts and is fully compatible with both in vitro and in cell transcription. Spectroscopic characterization shows that the incorporation rate of the cytosine analogue is on par with its natural counterpart. Using live cell imaging and flow cytometry, labelled mRNAs are efficiently and correctly translated upon transfection into living cells and cell-free systems. The spectral properties of the modified transcripts and their correct translation product allow for their straightforward and simultaneous visualization. This technology therefore offers a general route to understanding the biological behaviour of RNA of interest, including RNA based drugs. The fluorescent tricyclic cytosine analogue has formula (I):

##STR00001##

This specification discloses a novel methodology for labelling RNA via enzymatic incorporation of a minimally perturbing fluorescent tricyclic cytosine analogue. This analogue is shown to be 100% incorporated in example transcripts and is fully compatible with both in vitro and in cell transcription. Spectroscopic characterization shows that the incorporation rate of the cytosine analogue is on par with its natural counterpart. Using live cell imaging and flow cytometry, labelled mRNAs are efficiently and correctly translated upon transfection into living cells and cell-free systems. The spectral properties of the modified transcripts and their correct translation product allow for their straightforward and simultaneous visualization. This technology therefore offers a general route to understanding the biological behaviour of RNA of interest, including RNA based drugs. The fluorescent tricyclic cytosine analogue has formula (I):

##STR00001##

Provided are immune cell RNA sequencing methods. In some embodiments, the methods comprise producing a circularized DNA comprising a complementary DNA (cDNA) and a known heterologous sequence, wherein the cDNA is produced from an immune cell RNA. Such methods further comprise performing rolling circle amplification using the circularized DNA as template to produce a concatemer comprising repeating segments comprising the cDNA and the known heterologous sequence. Such methods further comprise sequencing the concatemer or fragments thereof. Also provided are methods comprising producing immune cell RNA sequencing reads using a R2C2 sequencing method, extracting HLA reads from the sequencing reads, and producing allele-specific HLA sequences from the extracted HLA reads. Also provided are computer-readable media, systems, compositions and kits that find use, e.g., in practicing the methods of the present disclosure.