Abstract: The present invention relates to molecular microscopy or volumetric imaging by proximal unique molecular identifiers (“UID”) reaction (“VIPUR”) microscopy methods to record the cellular co-localization and/or spatial distributions of arbitrary nucleic acid sequences, or other biomolecules tagged with nucleic sequences. The method involves one or both of two DNA sequence-components such as an ?-UID, which may identify the targeted sequences-of-interest themselves and/or spatial beacons relative to which their distances are measured, and a- ?-UID, which labels ?-UID association events.

Abstract: The invention provides methods for identifying binding partners (e.g., peptide ligands) that binds to a target protein (e.g., a cellular receptor). The methods entail co-localized expression of the target protein and candidate binding partners, and selection of binding partners based on their proximity in the plasma membrane.

Abstract: A method for evaluating in vitro the effect of a xenobiotic (e.g., a drug) on drug metabolism in hepatocytes. The kit comprises a first culture of hepatocytes, a portion of in vitro xenobiotic-stimulated biological sample, and instructions for incubating the first culture of hepatocytes with the portion of in vitro xenobiotic-stimulated biological sample, and analyzing the activity, expression, or a combination thereof of a biomarker in the hepatocytes to evaluate the effect of the xenobiotic on drug metabolism in the hepatocytes.

Abstract: Provided herein are methods, systems, kits and compositions for identifying nucleic acids of interest from individual cells. The methods include isolating single cells on electrodes and identifying nucleic acids of interest from the isolated cells by sequencing.

Abstract: The present disclosure provides methods, device, assemblies, and systems for dispensing and visualizing single cells. For example, provided herein are systems and methods for dispensing a dispense volume into a plurality of wells of a multi-well device, where, on average, a pre-determined number of cells (e.g., 1-20) are present in the dispense volume, and determining, via a cellular label, the number of cells present in each of the plurality of wells. Such dispensing and cell detection may be repeated a number of times with respect to wells identified as having less than the pre-determined number of cells in order increase the number wells in the multi-well device containing the desired number (e.g., a single cell).

Abstract: Presented herein are methods and compositions for analyzing rare nucleic acid species. Some methods presented herein use DNA reassociation kinetics following thermal denaturation to define populations of nucleic acid sequences, e.g., highly abundant (e.g., cDNA from rRNA), moderately abundant, and less abundant or rare sequences (e.g., cDNA from mRNA).

Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.

Abstract: An apparatus configured for improving retention of non-adherent cells is disclosed. The apparatus includes a plate that includes a number of elements having a first surface energy arranged in an array with an overlay, on the plate, having a second surface energy. The first surface energy results in a hydrophilic surface and the second surface energy results in a hydrophobic surface. A diameter of the elements is at least 1 mm. A height of the overlay having the second surface energy, which results in a hydrophobic surface, is between 5% and 100% of the diameter of the elements. The apparatus also includes a wall circumferential to the plate. A method for performing multiple reactions with the apparatus is also disclosed.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: A method of determining variation between a query cell culture media and a reference cell culture media is provided. The method comprises the steps of incubating a reference cell with an aliquot of the query culture media and at least three chemical cell stressors in wells of a microtitre plate and determining an environmental response of the reference cell in the presence of the query cell culture media and each of the plurality of chemical cell stressors. A query cell culture media specific environmental response fingerprint is generated comprising the plurality of chemical cell stressor specific environmental responses. The query cell culture media-specific environmental response fingerprint is compared with a reference media-specific environmental response fingerprints corresponding to a reference cell culture media and generated using the reference cell.

Abstract: The present invention generally relates to microfluidics and labeled nucleic acids. For example, certain aspects are generally directed to systems and methods for labeling nucleic acids within microfluidic droplets. In one set of embodiments, the nucleic acids may include “barcodes” or unique sequences that can be used to distinguish nucleic acids in a droplet from those in another droplet, for instance, even after the nucleic acids are pooled together. In some cases, the unique sequences may be incorporated into individual droplets using particles and attached to nucleic acids contained within the droplets (for example, released from lysed cells). In some cases, the barcodes may be used to distinguish tens, hundreds, or even thousands of nucleic acids, e.g., arising from different cells or other sources.

Abstract: A method for detecting an interaction between one or more protein bait and one or more candidate prey in a eukaryotic cell, comprising the steps of: a) providing an eukaryotic cell expressing (i) one or more protein bait, and (ii) one or more candidate prey, wherein said protein bait comprises a bait moiety and a polymerized-tubulin binding moiety. b) determining the occurence of an interaction between said one or more protein bait and said one or more candidate prey in the eukaryotic cell, wherein said protein bait is bound to polymerized tubulin in the eukaryotic cell, thereby localizing said one or more candidate prey along said polymerized tubulin, thereby detecting said interaction.

Abstract: The present disclosure provides for systems, devices, products, and methods for detecting and identifying microbial organisms in a sample as well as testing antimicrobial susceptibility of microbial organisms.

Abstract: A library of cell strains is characterized by culturing cells at spatially defined and separated positions in a culturing device (1) and determining a phenotypic characteristic of each cell strain in the culturing device (1). The cells are fixated at the spatially defined and separated positions in the culturing device (1) followed by in situgenotyping a respective variable region (150) of each cell strain at the spatially defined and separated positions in the culturing device (1). Each respective phenotypic characteristic is connected to each respective genotype based on the spatially defined and separated positions in the culturing device (1).

Abstract: The present invention provides a primer for nucleic acid random fragmentation and a nucleic acid random fragmentation method. The primer consists of a plurality of upstream random primers and downstream random primers. The sequence composition of the upstream random primers is 5?-X-Y-3?, and the sequence composition of the downstream random primers is 5?-P-Y?-X?-close-3?, wherein Y and Y? are random sequences, X is all or part of sequences of a sequencing platform 5? end adaptor, X? is all or part of sequences of a sequencing platform 3? end adaptor, P is phosphorylation modification, and close is close modification. The primer of the present invention adopts double random anchoring of both the upstream random primers and the downstream random primers, and a DNA sample can be randomly broken.

Abstract: The invention provides in situ nucleic acid sequencing to be conducted in biological specimens that have been physically expanded. The invention leverages the techniques for expansion microscopy (ExM) to provide new methods for in situ sequencing of nucleic acids as well as new methods for fluorescent in situ sequencing (FISSEQ) in a new process referred to herein as “expansion sequencing” (ExSEQ).

Abstract: This disclosure provides methods and devices for the label-free detection of target molecules of interest. The principles of the disclosure are particularly applicable to the detection of biological molecules (e.g., DNA, RNA, and protein) using standard SiO2-based microarray technology.

Abstract: The present invention provides a formulation to link protein to a solid support that comprises one or more proteins, Oligo-dT and one or more non-volatile, water-soluble protein solvents, solutes or combination thereof in an aqueous solution. Further provided is a method of attaching a protein to a surface of a substrate. The formulations provided herein are contacted onto the substrate surface, printed thereon and air dried. The substrate surface is irradiated with UV light to induce thymidine photochemical crosslinking via the thymidine moieties of the Oligo-dT.

Abstract: Methods of identifying target binding molecules by target guided synthesis are provided. The methods include providing two or more fragments capable of reacting to form the target binding molecule and mixing the fragments with the target. The methods can be used to identify target binding molecules that bind targets such as proteins or nucleic acids, including those that bind shallow binding pockets on the surface of such targets. The methods are applied to the Bcl-XL and Mcl-1 proteins from the Bcl-2 family of proteins. Using thio acid and sulfonyl azide fragments capable of reacting through sulfo-click chemistry, new acyl sulfonamides are identified that bind one or both of the Bcl-XL and Mcl-1 proteins. Pharmaceutical formulations of these target binding molecules are also provided.

Abstract: Provided are a vesicular linker and a single-chain cyclic library constructed by using the linker. The library can be used for RNA sequencing and other sequencing platforms dependent on a single-stranded cyclic library, and has the advantages of high throughput sequencing, high accuracy and simple operations.