The present invention generally relates to a combination of molecular barcoding and emulsion-based microfluidics to isolate, lyse, barcode, and prepare nucleic acids from individual cells in a high-throughput manner.

The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.

The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.

Provided is a gene target region enrichment method and a kit. The method comprises (1) amplifying fragmented DNA comprising a target region by means of a specific probe so as to obtain a captured-extension product, wherein the specific probe comprises a sequence complementary to the target region of the fragmented DNA, and the 3′ terminal nucleotide of the specific probe is modified to prevent a ligation reaction at the 3′ terminal of the specific probe; and (2) linking the 3′ terminal of the captured-extension product obtained in step (1) to linker DNA to obtain a ligation product.

Provided is a gene target region enrichment method and a kit. The method comprises (1) amplifying fragmented DNA comprising a target region by means of a specific probe so as to obtain a captured-extension product, wherein the specific probe comprises a sequence complementary to the target region of the fragmented DNA, and the 3′ terminal nucleotide of the specific probe is modified to prevent a ligation reaction at the 3′ terminal of the specific probe; and (2) linking the 3′ terminal of the captured-extension product obtained in step (1) to linker DNA to obtain a ligation product.

The invention generally relates to using linked target capture probes to profile the adaptive immune system of a subject, detect pathogens, perform spatial sequencing, and isolate mutant sequences.

The invention generally relates to using linked target capture probes to profile the adaptive immune system of a subject, detect pathogens, perform spatial sequencing, and isolate mutant sequences.

The present invention provides methods, antibodies and kits for detecting and/or quantifying expression of both non-nucleic acid molecules, such as proteins, and nucleic acid molecules in a single sample or single cell. The antibody is covalently conjugated to an oligonucleotide, such as a single-stranded DNA molecule, which comprises an identification tag and a blocking group, such as a ddNTP or an inverted dTTP, which prevents extension of the oligonucleotide by a polymerase. The method comprises the steps of reverse transcribing the conjugated oligonucleotide and the target nucleic acid simultaneously, amplifying both transcription production, and detecting the amplicons thereof. The method is also useful for detecting and/or quantifying the number of cells in a sample expressing a given non -nucleic acid molecule (e.g. protein).

The present invention provides methods, antibodies and kits for detecting and/or quantifying expression of both non-nucleic acid molecules, such as proteins, and nucleic acid molecules in a single sample or single cell. The antibody is covalently conjugated to an oligonucleotide, such as a single-stranded DNA molecule, which comprises an identification tag and a blocking group, such as a ddNTP or an inverted dTTP, which prevents extension of the oligonucleotide by a polymerase. The method comprises the steps of reverse transcribing the conjugated oligonucleotide and the target nucleic acid simultaneously, amplifying both transcription production, and detecting the amplicons thereof. The method is also useful for detecting and/or quantifying the number of cells in a sample expressing a given non -nucleic acid molecule (e.g. protein).

The present disclosure provides methods for optimizing barcode design for multiplex DNA sequencing. Also disclosed are DNA barcodes optimized for use with particular sequencing technologies.