Abstract: The present disclosure relates to methods and compositions for enhanced assessment of exogenous polynucleotide and/or polypeptide-mediated transcriptional perturbations at high throughput and single cell/droplet levels of resolution. In embodiments, nucleic acid fusions of exogenous polynucleotide(s) and associated target transcript(s) are produced within individually sequestered or discretely identifiable cells/lysates and analyzed for exogenous polynucleotide mediated perturbations across a vast population of droplets/cells within individual reactions. Kits for performance of the methods are also provided.

Abstract: The present invention relates to the analysis of complex single cell sequencing libraries. Disclosed are methods for enrichment of library members based on the presence of cell-of origin barcodes to identify and concentrate DNA that is relevant to interesting cells or components that would be expensive or difficult to study otherwise. Also, disclosed are methods of capturing cDNA library molecules by use of CRISPR systems, hybridization or PCR. The present invention allows for identifying the properties of rare cells in single cell RNA-seq data and accurately profile them through clustering approaches. Further information on transcript abundances from subpopulations of single cells can be analyzed at a lower sequencing effort. The methods also allow for linking TCR alpha and beta chains at the single cell level.

Abstract: The present invention provides for methods to obtain multiple information-rich samples at different time points from the same cell while minimally disrupting the cell. The subject matter disclosed herein is generally related to nucleic acid constructs for continuous monitoring of live cells. Specifically, the subject matter disclosed herein is directed to nucleic acid constructs that encode a fusion protein and a construct RNA sequence that induce live cells to self-report cellular contents while maintaining cell viability. The present invention may be used to monitor gene expression in single cells while maintaining cell viability.

Abstract: The subject matter disclosed herein is generally directed to methods and compositions for stable transduction of target cells with libraries of genetic elements. The invention reduces intermolecular recombination between library elements and integration of multiple genetic elements.

Abstract: A method for detecting oncogenic growth and viability, and/or degree of cellular transformation and/or identifying an agent that inhibits cellular transformation is disclosed. The method including: providing a cellular sample, such as a sample of cells obtained from a subject or a cell line; culturing the cellular sample in low attachment conditions; and detecting growth and7or cell viability of the sample, wherein increased growth relative and/or viability relative to a control or control level indicative of basal growth and/or viability indicates cellular transformation. In some embodiments, the method includes introducing a n expression vector into cells of the cellular sample, wherein the expression vector comprises a gene product expression sequence being tested for transformation ability. In some embodiments the cellular sample is contacted with a test agent and growth and/or cell viability of the sample is determined to determine if the agent inhibits transformation.

Abstract: The present disclosure relates compositions and methods for combinatorial drug discovery in nanoliter droplets. More particularly, the disclosure relates to novel synergistic agents that increase efficacy of antibiotic agents to treat bacterial infection.

Abstract: The present disclosure relates to compositions and methods for nucleic acid sequencing, and specifically, at least in certain aspects, provides methods and compositions for enhancing the efficacy, throughput and/or yield of known long-range sequencing platforms, by providing chimeric arrays of input sequences. Such arrays of component nucleic acid sequence elements can be prepared via methods that minimize introduction of bias. The application of the current methods to obtain isoform sequencing information, e.g., from patient samples is specifically also provided, as are methods for mitochondrial lineage tracing that employ the instant chimeric amplicon sequencing processes. Methods and systems for array nucleic acid sequence processing and interpretation are also provided.

Abstract: The present invention provides for methods to obtain multiple information-rich samples at different time points from the same cell while minimally disrupting the cell. The subject matter disclosed herein is generally related to nucleic acid constructs for continuous monitoring of live cells. Specifically, the subject matter disclosed herein is directed to nucleic acid constructs that encode a fusion protein and a construct RNA sequence that induce live cells to self-report cellular contents while maintaining cell viability. The present invention may be used to monitor gene expression in single cells while maintaining cell viability.

Abstract: The present invention relates to the analysis of complex single cell sequencing libraries. Disclosed are methods for enrichment of library members based on the presence of cell-of origin barcodes to identify and concentrate DNA that is relevant to interesting cells or components that would be expensive or difficult to study otherwise. Also, disclosed are methods of capturing cDNA library molecules by use of CRISPR systems, hybridization or PCR. The present invention allows for identifying the properties of rare cells in single cell RNA-seq data and accurately profile them through clustering approaches. Further information on transcript abundances from subpopulations of single cells can be analyzed at a lower sequencing effort. The methods also allow for linking TCR alpha and beta chains at the single cell level.

Abstract: The present disclosure relates to compositions and methods for single-cell nucleic acid sequencing, and specifically provides for pre-amplifying target nucleic acids in a manner that allows for more proportionate detection of all target nucleic acids, including low prevalence/abundance RNAs, from individual cells. The disclosure also provides for application of a series of barcoding steps to associate cell-specific identifiers (IDs) to the targeted nucleotide sequences, and ultimately provides for increased throughput capacity and greater accuracy of single-cell nucleic acid sequencing. Certain aspects of the present disclosure also provide for improved quantitative detection of nucleic acid sequence barcodes, which in embodiments allows for highly sensitive quantitative detection of barcoded antibody levels and/or highly sensitive quantitative detection of barcoded antibody-bound protein levels (e.g.

Abstract: The subject matter disclosed herein is generally directed to methods and compositions for tagging cells of interest, tracking evolution of the tagged cells, and recovering the original tagged cells for further study. Specifically, cells are tagged with a DNA construct encoding a barcode sequence comprising a guide sequence. Barcoded cells can then be recovered using a reporter construct having CRISPR target sequences specific for the cell having a barcode of interest.

Abstract: Compositions and methods for combinatorial drug discovery in nanoliter droplets are described. Novel synergistic agents that increase efficacy of antibiotic agents to treat bacterial infection are disclosed.

Abstract: The subject matter disclosed herein is generally directed to methods and compositions for tagging cells of interest, tracking evolution of the tagged cells, and recovering the original tagged cells for further study. Specifically, cells are tagged with a DNA construct encoding a barcode sequence comprising a guide sequence. Barcoded cells can then be recovered using a reporter construct having CRISPR target sequences specific for the cell having a barcode of interest.

Abstract: Embodiments disclosed herein provide reagents and methods for high-throughput screening of nucleic acid sequence variations in nucleic acid containing specimens. Nucleic acid specimens to be screened are loaded into separate discrete volumes. Optically encoded particles are used to deliver primers to amplify one or more sequences comprising the nucleic acid sequence variation. The optically encoded particles may be delivered to the discrete volumes randomly resulting in a random combination of optically encoded particles in each well, or a unique combination of optically encoded particles may be specifically assigned to each discrete volume. The observable combination of optically encoded particles may then be used to identify each discrete volume.

Abstract: The subject matter disclosed herein is generally directed to methods and compositions for stable transduction of target cells with libraries of genetic elements. The invention reduces intermolecular recombination between library elements and integration of multiple genetic elements.

Abstract: The present invention relates to methods of quantifying, amplifying, or preparing nucleic acid molecules, where the methods involve contacting a sample to be tested with nucleic acid molecule amplification reaction components and a label to form a reaction sample. The methods further involve partitioning the reaction sample into droplets or a gel and allowing nucleic acid molecule amplification to occur.

Abstract: The microfluidic devices and systems disclosed herein reduce sample loss and help decrease sample processing bottlenecks for applications such as next generation sequencing (NGS). The microfluidic devices include a plurality of reaction modules. Each reaction module may comprise one or more reaction circuits. Each reaction circuit may comprise a single reaction flow channel with each reaction circuit connected by a bridge flow channel. Alternatively, each reaction circuit may comprise two or more reaction flow channels connected by two or more bridge flow channels. The combination of any two bridge flow channels and a portion of the two or more reaction flow channels between the any two bridge flow channels defining may define the reaction circuit. The reaction module may be arranged as nodes connected by bridge flow channels or each reaction module may be arranged in a parallel fashion on the microfluidic device.

Abstract: Embodiments disclosed herein provide reagents and methods for high-throughput screening of nucleic acid sequence variations in nucleic acid containing specimens. Nucleic acid specimens to be screened are loaded into separate discrete volumes. Optically encoded particles are used to deliver primers to amplify one or more sequences comprising the nucleic acid sequence variation. The optically encoded particles may be delivered to the discrete volumes randomly resulting in a random combination of optically encoded particles in each well, or a unique combination of optically encoded particles may be specifically assigned to each discrete volume. The observable combination of optically encoded particles may then be used to identify each discrete volume.

Abstract: The microfluidic devices and systems disclosed herein reduce sample loss and help decrease sample processing bottlenecks for applications such as next generation sequencing (NGS). The microfluidic devices include a plurality of reaction modules. Each reaction module may comprise one or more reaction circuits. Each reaction circuit may comprise a single reaction flow channel with each reaction circuit connected by a bridge flow channel. Alternatively, each reaction circuit may comprise two or more reaction flow channels connected by two or more bridge flow channels. The combination of any two bridge flow channels and a portion of the two or more reaction flow channels between the any two bridge flow channels defining may define the reaction circuit. The reaction module may be arranged as nodes connected by bridge flow channels or each reaction module may be arranged in a parallel fashion on the microfluidic device.

Abstract: The present disclosure relates to compositions and methods for combinatorial assessment of nanoscale droplets, as specifically exemplified by massively parallel assessment of spatially-directed (while agnostic as to precise droplet content) combinations of droplets harboring distinct and independently identifiable microbial types and/or chemical compounds or mixtures. More particularly, the disclosure relates to a platform and methodologies for identifying advantageous (including synergistic, additive, etc.) microbial interactions and/or chemical compound or mixture interactions with microbes in a manner that allows for binary, trinary, etc. combinatorial assessments to be performed across a range of many discrete input types of microbes (e.g., 6-16 or more discrete input microbial types), to an extent capable of approaching comprehensive sampling and measurement of microbial community combinations from a selected panel of microbial inputs, optionally also in the presence of chemical compounds or mixtures (e.