Provided are methods for profiling cellular analytes of a cell by barcoding the cell in a combinatorial split and pool iterative process. In some instances, a cell bead may be generated from the cell, and the analytes therein barcoded in a combinatorial split and pool iterative process while the analytes are retained in the cell bead during iterative partitioning.

A system and method are provided for simplifying and accelerating the screening and characterization of molecular interactions by high-throughput functional screening and sequencing of single cells. More specifically, a platform is provided which combines a solid support and an innovative method for capturing and barcoding of nucleic acids that allows simultaneous phenotyping and genotyping of >100, 000s of cells.

A system and method are provided for simplifying and accelerating the screening and characterization of molecular interactions by high-throughput functional screening and sequencing of single cells. More specifically, a platform is provided which combines a solid support and an innovative method for capturing and barcoding of nucleic acids that allows simultaneous phenotyping and genotyping of >100, 000s of cells.

Single-cell multi-omics by co-encapsulating a single cell with two beads, the first an RNA barcoding bead having barcoded mRNA capture primer oligonucleotides attached on the bead surface; and the second a DNA barcoding bead having two types of oligonucleotides releasably attached to the surface: (1) barcoded adapter oligonucleotides that are complementary to oligonucleotides bound to the transposase that are eventually incorporated into gDNA fragments and (2) polyadenylated barcoded oligonucleotides containing the same barcode sequence as the adapters. In addition, integrated analysis of RNA and protein, including intracellular protein, from individual cells using similar co-encapsulation of a single cell, an RNA barcoding bead, and with/without a specific or non-specific protein binding bead in a microwell, to avoid protein fixation by first lysing the cell to liberate intracellular contents, and then capturing protein either on a solid surface or in solution with barcoded affinity reagents.

Single-cell multi-omics by co-encapsulating a single cell with two beads, the first an RNA barcoding bead having barcoded mRNA capture primer oligonucleotides attached on the bead surface; and the second a DNA barcoding bead having two types of oligonucleotides releasably attached to the surface: (1) barcoded adapter oligonucleotides that are complementary to oligonucleotides bound to the transposase that are eventually incorporated into gDNA fragments and (2) polyadenylated barcoded oligonucleotides containing the same barcode sequence as the adapters. In addition, integrated analysis of RNA and protein, including intracellular protein, from individual cells using similar co-encapsulation of a single cell, an RNA barcoding bead, and with/without a specific or non-specific protein binding bead in a microwell, to avoid protein fixation by first lysing the cell to liberate intracellular contents, and then capturing protein either on a solid surface or in solution with barcoded affinity reagents.

The present disclosure provides methods, systems, and kits for detecting molecules in a sample with a pre-equilibrium digital immunoassay. The methods and systems provide means for quantifying molecules in a biological sample of minimal volume in short amounts of time.

The present disclosure provides methods, systems, and kits for detecting molecules in a sample with a pre-equilibrium digital immunoassay. The methods and systems provide means for quantifying molecules in a biological sample of minimal volume in short amounts of time.

The present disclosure relates to compositions and methods for assessing relative DNA levels (e.g., levels of genomic DNA, mtDNA, viral DNA, bacterial DNA, etc.) in a spatially-defined manner across a tissue sample, specifically providing DNA sequence identity and relative abundance information at high-resolution across multiple locations assessed across the tissue sample.

The present disclosure relates to compositions and methods for assessing relative DNA levels (e.g., levels of genomic DNA, mtDNA, viral DNA, bacterial DNA, etc.) in a spatially-defined manner across a tissue sample, specifically providing DNA sequence identity and relative abundance information at high-resolution across multiple locations assessed across the tissue sample.

The present disclosure relates to a method of sequencing nascent RNA in a cell. In some embodiments, the nascent RNA is conjugated to DNA using copper-catalyzed azide-alkyne cycloaddition (CuAAC). Methods of the present disclosure can be used to generate genomic libraries of a cell and measure gene expression and enhancer and/or super-enhancer activity.