This disclosure provides a decentralized workflow for analyzing single cell gene expression. The workflow makes use of pre-templated instant partitions to segregate cells into separate compartments to individually capture and barcode RNA from single cells in a massively parallel single tube format. The workflow includes steps for processing the RNA from the single cells for sequencing. Separate portions of the decentralized workflow are performed by a research lab and a core facility, allowing increased flexibility in time and location of protocol steps.

This disclosure provides a powerful screening platform that combines pre-templated instant partitions with DNA-encoded library (DEL) technologies to identify target small molecule interactions and analyze their intracellular effects in single cell resolution using methods that require minimal sample preparation and affordable sequencing costs.

This disclosure provides a powerful screening platform that combines pre-templated instant partitions with DNA-encoded library (DEL) technologies to identify target small molecule interactions and analyze their intracellular effects in single cell resolution using methods that require minimal sample preparation and affordable sequencing costs.

Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.

The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs or organisms. In some embodiments, through sequential barcoding, the present invention provides methods for high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci.

Systems and methods for associating single cell imaging data with RNA transcriptomics. Single cells are isolated into microwells with a microbead having oligonucleotides conjugated on its surface. Each oligonucleotide includes a cell identifying optical barcode that is unique to that bead and binding sequence for RNA capture after cell lysis. The system is configured for loading single cells into the microarray and for flowing cell lysis buffers and other reagents into the microarray for performing RNA library sample preparation. The system is also configured for lowing optical hybridization probes that are complementary to the cell identifying optical barcodes and optically labeled onto the microwell array and for obtaining images of the microwells in response to the probes. The system and unique cell identifying optical barcodes and complementary optical hybridization probes facilitate a link between phenotypic imaging of cells resident on the microwell array with single cell whole transcriptome sequencing.

The present disclosure generally relates to spatial detection of a nucleic acid, such as a genomic DNA or a RNA transcript, in a cell comprised in a tissue sample. The present disclosure provides methods for detecting and/or analyzing nucleic acids, such as chromatin or RNA transcripts, so as to obtain spatial information about the localization, distribution or expression of genes in a tissue sample. The present disclosure thus provides a process for performing “spatial transcriptomics” or “spatial genomics,” which enables the user to determine simultaneously the expression pattern, or the location/distribution pattern of the genes expressed or genes or genomic loci present in a single cell while retaining information related to the spatial location of the cell within the tissue architecture.

The disclosure provides variants of nicotine oxidoreductase and methods to select such variants that are unexpectedly active in the catabolic destruction of nicotine by oxidation using oxygen as electron acceptor, and catabolically active fragments thereof. Also disclosed are compositions comprising the CycN cytochrome c protein and at least one of the variant nicotine oxidoreductase holoenzymes, the fragments thereof, or a naturally occurring nicotine oxidoreductase, as well as fusion proteins comprising catalytically active nicotine oxidoreductase fragments or holoenzymes and CycN cytochrome c fragments or holoenzymes. Additionally, variants of L-6-hydroxynicotine oxidase, or catalytically active fragments thereof, are provided. Further disclosed are polynucleotides encoding such proteins, vectors comprising such polynucleotides, and host cells comprising such polynucleotides or vectors. Also provided are methods of using any of the disclosed compositions or formulations to treat nicotine dependence or reduce the risk of relapse to nicotine dependence.

Food distributed to consumers through a distribution chain may be traced by tagging the food with DNA tags that identify the origin of the food, such as the grower, packer and other points of distribution, and their attributes. This makes it much quicker and easier to trace the food in case of food contamination or adulteration. Preferably these attributes indicate the field, location, crew and machine used to grow and process the food, and the dates of the various steps of food harvesting, processing and distribution. Natural or synthetic DNA pieces may be used to tag items, including food items. Multidigit binary or other types of bar codes may be represented by multiple types of DNA. Each digit of the bar code may be represented by one, two or more unique DNA pieces.

This disclosure provides methods for determining relative abundance of one or more non-host species in a sample from a host. Also provided are methods involving addition of known concentrations of synthetic nucleic acids to a sample and performing sequencing assays to identify non-host species such as pathogens. Also provided are methods of tracking samples, tracking reagents, and tracking diversity loss in sequencing assays.