Disclosed is a method of quality control of nucleic acid amplification using quality control oligonucleotide. The method comprises a nucleic acid detection step and a determination step. The nucleic acid detection step comprises the steps of: preparing a nucleic acid sample containing a target nucleic acid and a quality control polynucleotide; preparing a compartment containing one molecule of the target nucleic acid and a compartment containing one molecule of the quality control polynucleotide; and carrying out nucleic acid amplification of the target nucleic acid and the quality control polynucleotide, in the compartments, and carrying out signal detection using a detection probe to detect a signal originated from the detection probe. In the determination step, it is determined as to whether or not the nucleic acid detection step is proper on the basis of the result obtained in the signal detection step.

Disclosed is a method of quality control of nucleic acid amplification using quality control oligonucleotide. The method comprises a nucleic acid detection step and a determination step. The nucleic acid detection step comprises the steps of: preparing a nucleic acid sample containing a target nucleic acid and a quality control polynucleotide; preparing a compartment containing one molecule of the target nucleic acid and a compartment containing one molecule of the quality control polynucleotide; and carrying out nucleic acid amplification of the target nucleic acid and the quality control polynucleotide, in the compartments, and carrying out signal detection using a detection probe to detect a signal originated from the detection probe. In the determination step, it is determined as to whether or not the nucleic acid detection step is proper on the basis of the result obtained in the signal detection step.

Disclosed herein are methods for single-cell sequencing. In some examples, the methods include enriching a sample comprising a plurality of cells for cells of interest to produce an enriched cell sample; isolating one or more cells of interest in the enriched cell sample; and obtaining sequence information of one or more polynucleotides from each of the one or more isolated cells. Obtaining sequence information may include generating a molecularly indexed polynucleotide library from the one or more isolated cells. Enriching the sample may include focusing cells of interest in the sample using acoustic focusing.

Disclosed herein are methods for single-cell sequencing. In some examples, the methods include enriching a sample comprising a plurality of cells for cells of interest to produce an enriched cell sample; isolating one or more cells of interest in the enriched cell sample; and obtaining sequence information of one or more polynucleotides from each of the one or more isolated cells. Obtaining sequence information may include generating a molecularly indexed polynucleotide library from the one or more isolated cells. Enriching the sample may include focusing cells of interest in the sample using acoustic focusing.

The present invention provides methods and tools for analyzing genetic interactions. The subject matter is generally directed to single-cell genomics and proteomics, including methods of performing genome-wide CRISPR perturbation screens and determining gene expression phenotypes.

The present invention provides methods and tools for analyzing genetic interactions. The subject matter is generally directed to single-cell genomics and proteomics, including methods of performing genome-wide CRISPR perturbation screens and determining gene expression phenotypes.

Provided herein, in some embodiments, are methods and compositions for detecting differentially expressed genes in a sample obtained from a subject having or at risk for preeclampsia.

In certain embodiments, the present invention provides a detection composition comprising a picodroplet comprising (a) an aqueous solution, and (b) a substrate probe comprising (i) an oligonucleotide of 2 to 75 nucleotides in length, (ii) a fluorophore operably linked to the oligonucleotide, and (iii) a quencher operably linked to the oligonucleotide. As used herein, the term picodroplet comprises a liquid droplet that has a volume of 0.014 to 2.6 picoliters. In certain embodiments, the present invention provides a method of detecting at least one individual nuclease molecule present in a sample, comprising contacting an aqueous sample suspected of containing at least one nuclease with at least one detection composition comprising a picodroplet comprising (a) an aqueous solution, and (b) a substrate probe comprising (i) an oligonucleotide of 2 to 75 nucleotides in length, (ii) a fluorophore operably linked to the oligonucleotide, and (iii) a quencher operably linked to the oligonucleotide to form an aqueous reaction mixture; emulsifying the aqueous mixture in oil to form picoliter-scale droplets in an emulsion, (c) incubating the picoliter-scale droplets in the emulsion in order for the nuclease, if present, to digest the substrate probes linked to the microbeads; recovering the microbeads; and detecting fluorescence emitting from the microbeads.

In certain embodiments, the present invention provides a detection composition comprising a picodroplet comprising (a) an aqueous solution, and (b) a substrate probe comprising (i) an oligonucleotide of 2 to 75 nucleotides in length, (ii) a fluorophore operably linked to the oligonucleotide, and (iii) a quencher operably linked to the oligonucleotide. As used herein, the term picodroplet comprises a liquid droplet that has a volume of 0.014 to 2.6 picoliters. In certain embodiments, the present invention provides a method of detecting at least one individual nuclease molecule present in a sample, comprising contacting an aqueous sample suspected of containing at least one nuclease with at least one detection composition comprising a picodroplet comprising (a) an aqueous solution, and (b) a substrate probe comprising (i) an oligonucleotide of 2 to 75 nucleotides in length, (ii) a fluorophore operably linked to the oligonucleotide, and (iii) a quencher operably linked to the oligonucleotide to form an aqueous reaction mixture; emulsifying the aqueous mixture in oil to form picoliter-scale droplets in an emulsion, (c) incubating the picoliter-scale droplets in the emulsion in order for the nuclease, if present, to digest the substrate probes linked to the microbeads; recovering the microbeads; and detecting fluorescence emitting from the microbeads.

Methods and systems for quantification of a target nucleic acid in a sample are provided. The method includes forming a plurality of discrete sample portions. Each of the plurality of discrete sample portions comprising a portion of the sample, and a reaction mixture. The method further includes amplifying the plurality of discrete sample portions to form a plurality of discrete processed sample portions. At least one discrete processed sample portion containing nucleic acid amplification reaction products. Fluorescence signals are detected from the at least one of the plurality of discrete processed sample portions to determine a presence of the at least one target nucleic acid. The method also includes determining the respective volumes of the plurality of the plurality of discrete processed sample portions, and estimating the number of copies-per-unit-volume of the at least one target nucleic acid in the sample. Estimating the number of copies-per-unit-volume is based on the number of discrete processed sample portions determined to contain the at least one target nucleic acid therein.