Abstract: This disclosure provides methods for preparing a sequencing library including the steps of providing a template nucleic acid sequence, dNTPs, dUTP, a primer, a polymerase, a dUTP excising enzyme, and a plurality of beads including oligonucleotide adapter sequence segments; amplifying the template nucleic acid with the polymerase, dNTPs, dUTP and random hexamer to provide a complementary nucleic acid sequence including occasional dUTPs; and excising the incorporated dUTPs with the dUTP excising enzyme to provide nicks in the complementary nucleic acid sequence to provide a sequencing library.

Abstract: The invention relates to a method for selecting a glycopolypeptide that binds to a target protein, the method including the steps of providing a pool of glycopolypeptides fused via puromycin linker to an encoding mRNA-cDNA duplex; combining the pool with a target protein to form a mixture; incubating the mixture for a period of time sufficient to allow any target protein to bind to one or more of the glycopolypeptides, thereby forming glycopolypeptide-target protein complexes; and isolating from the mixture the glycopolypeptide-target protein complexes, thereby identifying a plurality of selected glycopolypeptides.

Abstract: The present disclosure automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides are preferably expressed in the cells under conditions that provide both secretion and display of the engineered peptides on the cell surfaces, thus providing access of the engineered peptide antigens to identify potential TCR binding targets. The cell libraries cab be engineered using an automated editing system that provides for one or more targeted edits per cell.

Abstract: This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X?-A?-B?-Z?, wherein sequence A? is complementary to a genomic fragment and sequence B? is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.

Abstract: The present application relates to a system for designing promoters for selective expression of genes. Thereby identified transcription regulatory elements are selected according to a specific methodology and used to create a library of transcription regulatory elements, which are then used to construct specific promoters, especially tissue-specific promoters.

Abstract: The present disclosure methods for identifying binding partners using cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of peptides that bind to targets of interest. The engineered peptides are preferably expressed in the cells under conditions that provide both secretion and display of the engineered peptides on the cell surfaces, thus providing access of the engineered peptides to identify potential binding pairs. The cell libraries cab be engineered using an automated editing system that provides for one or more targeted edits per cell.

Abstract: The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of binding pairs. The engineered peptides may be displayed using various cell surface display technologies.

Abstract: A device and method detect cellular targets in a bodily source by utilizing a biofunctional pad comprised of a thin film of carbon nanotubes (CNT's). When antibodies are absorbed by the CNT's, cellular targets having markers matching the antibodies may be detected in a bodily source placed upon the biofunctional pad by measuring the conductivity of the thin film using conductive contacts electrically coupled to the thin film, as the binding of the receptors in the cellular targets to the antibodies changes the free energy in the thin film. In many respects, the device functions as a Field Effect Transistor (FET) with the bodily source, e.g., blood, acting as a polyelectrolyte liquid gate electrode to create a varying electrostatic charge or capacitance in the thin film based upon the binding of cellular targets in the source to the antibodies present on the biofunctional pad.

Abstract: Provided are methods for performing patterned chemistry and arrays prepared thereby.

Abstract: Provided herein are methods, compositions, and kits for targeted sequencing of polynucleotides with high accuracy and low amplification and sequencing errors.

Abstract: Method of localizing cells to at least one discrete area on a surface of a substrate by propelling droplets of an aqueous dispersion of a synthetic construct of the structure F-S-L from a plurality of orifices located in a print head of an inkjet printer onto the surface. In the structure F-S-L, F is a functional moiety capable of associating with the cells by direct or indirect non-covalent interaction with biotin or an epitope of an antigen presented at the surface of the cells, S is a spacer selected to provide a construct that is dispersible in water at a temperature of 25° C. in the absence of organic solvents or detergents, and L is a diacyl- or dialkyl lipid.

Abstract: Methods and systems for sample preparation techniques that allow amplification (e.g., whole genome amplification) and sequencing of chromatin accessible regions of single cells are provided. The methods and systems generally operate by forming or providing partitions (e.g., droplets) including a single biological particle and a single bead comprising a barcoded oligonucleotide. The preparation of barcoded next-generation sequencing libraries prepared from a single cell is facilitated by the transposon-mediated transposition and fragmentation of a target nucleic acid sequence. The methods and systems may be configured to allow the implementation of single-operation or multi-operation chemical and/or biochemical processing within the partitions.

Abstract: The stable and precise incorporation of multiple fluorescent dyes into hydrogel microparticles. The multiple fluorescent dyes, excited with the same source, have distinct fluorescence emission spectra to enable identification of the microparticles. The fluorescent molecules are directly polymerized into the hydrogel matrix or stably incorporated through molecular entanglement. By changing the molar ratios of the fluorescent dyes, different and identifiable microparticles can be synthesized.

Abstract: Compositions, devices, methods and systems are provided for differential functionalization of a surface of a structure to support biopolymer synthesis. Provided herein are processes which include use of lamps, lasers, and/or microcontact printing to add functional groups to surfaces for the efficient and uniform synthesis of oligonucleic acids.

Abstract: Molecular identity tags and methods of marking target nucleic acids with molecular identity tags for identifying intermolecular ligation products. Terminal regions of linear target nucleic acids are marked with pairs of distinguishable molecular identity tags. Each linear target nucleic acid is marked with only one distinguishable pair. The terminal ends of the marked target nucleic acids are joined to generate circularized nucleic acids, thereby juxtaposing two molecular identity tags across the joined terminal ends. Circularized nucleic acids or downstream products thereof comprising juxtaposed unpaired molecular identity tags constitute intermolecular nucleic acid products that can be identified and eliminated from subsequent analyses of the nucleic acids. The molecular identity tags may comprise physically linked and non-physically linked pairs. Physically linked molecular identity tags designed for production and analysis of mate-pair libraries with next-generation sequencing platforms are provided.

Abstract: Methods and compositions for making and isolating allosteric DNA binding proteins that bind to one or more allosteric effectors to induce a conformation change in the proteins are provided.

Abstract: A method for preparing a topographically structured hydrogel microarray is described comprising the steps of a) providing one or more types of biomolecule(s) on top of micropillars of an array of micropillars, preferably by means of robotical spotting, b) providing a partially crosslinked hydrogel on a substrate, preferably attached to a substantially rigid and/or planar substrate, c) simultaneously soft-embossing a hydrogel microwell array and transferring the biomolecule(s) from the micropillars to the microwells by pressing the micropillars of the array of step a) onto the partially crosslinked layer of hydrogel of step b) until substantial completion of crosslinking and d) demolding the array of micropillars of step a) from the hydrogel microwell array of step c).

Abstract: The present invention relates to a method of producing an oligomer array. The invention comprises the steps of: providing a substrate with a multitude of recesses; introducing a first particle with a first molecule into a recess; releasing the first molecule from the first particle; binding the first molecule to a second molecule to form an oligomer while immobilizing the second molecule in the recess; optionally repeating the steps, wherein at least one of the first particles and/or the first molecules comprises a detectable marker.

Abstract: A carrier to which is attached a peptide and DNA encoding the peptide, wherein the peptide includes at least one non-natural amino acid and/or wherein the peptide has a constrained secondary structure; or a carrier to which is attached ?2 microglobulin, a peptide, and DNA encoding the peptide, said carrier not bearing an MHC or MHC-like molecule.

Abstract: The present invention provides a diagnostic device allowing highly specific and efficient in vivo and/or in vitro detection of a bio marker in a broad range of bodily fluids or tissues. The diagnostic device is composed of a binding agent that specifically binds a bio marker present in the bodily fluid linked by a linker compound or layer to the substrate, which includes a metallic, a semiconductor, or a polymeric carrier. The present invention further provides methods using said device for the detection of bio markers, as well as kits comprising said device and suitable ingredients for the detections of bio markers in a bodily fluid. Furthermore, the invention provides suitable in vivo and in vitro applications of said binding agent for the detection of specific disease-related target structures.