Abstract: Provided herein are compositions and methods for generating phase-shift barcode oligonucleotides for library construction for next-generation sequencing. In some cases, barcode oligonucleotides are attached to particles or beads. Also provided are methods and kits for using the phase-shift barcode oligonucleotides in sequencing assays.

Abstract: Microfluidic methods of altering the spacing of a stream of objects. In an exemplary method, objects of the object stream may be transported in carrier fluid along a microfluidic channel structure having an inflow region, an outflow region, and an expanded region extending from the inflow region to the outflow region. The expanded region may have a greater cross-sectional area for fluid flow than each of the inflow region and the outflow region. Objects of the object stream may be moved from the inflow region to the expanded region such that at least a subset of such objects are moved closer to one another. Objects of the object stream may be passed from the expanded region to the outflow region to increase a distance between such objects.

Abstract: The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes

Abstract: Methods for determining a location of a feature on an array include: (a) providing a first array with a first plurality of features immobilized on a first substrate; (b) providing a second array with a second plurality of features immobilized on a second substrate; (c) aligning the first array with the second array; (d) hybridizing a first barcoded oligonucleotide of the first array to a second barcoded oligonucleotide of the second array, thereby producing a combined nucleic acid that includes first and second spatial barcodes; (e) determining all or a portion of the sequence of the combined nucleic acid; and (f) identifying the second barcoded oligonucleotide associated with the first barcoded oligonucleotide in the combined nucleic acid, and determining the location of a second feature in the second array.

Abstract: This disclosure describes apparatus, systems, methods, kits, and compositions for spatial analysis of biological samples. In particular, the present disclosure provides for spatial profiling of a biological analyte present in a cell-containing biological sample.

Abstract: Methods for determining a location of a feature in a spatial array with features include: (a) providing an array with a first set of one or more features immobilized on a substrate, a first feature of the first set having a first barcoded oligonucleotide with a first spatial barcode and a first constant sequence, and a second set of one or more features immobilized on the substrate, a second feature of the second set having a second barcoded oligonucleotide with a second spatial barcode and a second constant sequence; (b) attaching the first constant sequence to the second constant sequence to generate a nucleic acid product; (c) determining all or a portion of a sequence of the nucleic acid product or a complement thereof; and (d) associating the second barcoded oligonucleotide with the first barcoded oligonucleotide in the nucleic acid product.

Abstract: Provided herein are methods of determining a location of a biological analyte in a biological sample.

Abstract: This disclosure relates to methods of manufacturing of spatial arrays and determining the location of an analyte present in a biological sample (e.g., by utilizing a cell-tagging agent).

Abstract: This disclosure relates to compositions and methods for generating a spatial array.

Abstract: Microfluidic methods of altering the spacing of a stream of objects. In an exemplary method, objects of the object stream may be transported in carrier fluid along a microfluidic channel structure having an inflow region, an outflow region, and an expanded region extending from the inflow region to the outflow region. The expanded region may have a greater cross-sectional area for fluid flow than each of the inflow region and the outflow region. Objects of the object stream may be moved from the inflow region to the expanded region such that at least a subset of such objects are moved closer to one another. Objects of the object stream may be passed from the expanded region to the outflow region to increase a distance between such objects.

Abstract: Provided herein are compositions and methods for generating phase-shift barcode oligonucleotides for library construction for next-generation sequencing. In some cases, barcode oligonucleotides are attached to particles or beads. Also provided are methods and kits for using the phase-shift barcode oligonucleotides in sequencing assays.

Abstract: Microfluidic systems and methods for arranging a set of objects. In an exemplary method, the set of objects may be transported in carrier fluid along a microfluidic channel structure having a reformatting zone including an object-accessible region and at least one object-excluding region. A portion of the carrier fluid may be moved from the object-accessible region to the at least one object-excluding region in an upstream section of the reformatting zone, to reduce a spacing of objects of the set. The portion of the carrier fluid may be directed into the object-accessible region from the at least one object-excluding region in a downstream section of the reformatting zone, to increase a spacing of objects of the set. The steps of moving and directing in combination may increase the spacing between objects disproportionately for a subset of the objects that are closest to one another.

Abstract: Provided herein are compositions and methods for generating phase-shift barcode oligonucleotides for library construction for next-generation sequencing. In some cases, barcode oligonucleotides are attached to particles or beads. Also provided are methods and kits for using the phase-shift barcode oligonucleotides in sequencing assays.

Abstract: Provided herein are methods of determining a location of a biological analyte in a biological sample.

Abstract: Provided herein are compositions and methods for generating phase-shift barcode oligonucleotides for library construction for next-generation sequencing. In some cases, barcode oligonucleotides are attached to particles or beads. Also provided are methods and kits for using the phase-shift barcode oligonucleotides in sequencing assays.

Abstract: Provided herein are compositions and methods for generating phase-shift barcode oligonucleotides for library construction for next-generation sequencing. In some cases, barcode oligonucleotides are attached to particles or beads. Also provided are methods and kits for using the phase-shift barcode oligonucleotides in sequencing assays.

Abstract: Methods of assessing whether multiple differently-barcodes primers are in partitions are provided.

Abstract: Microfluidic systems and methods for arranging a set of objects. In an exemplary method, the set of objects may be transported in carrier fluid along a microfluidic channel structure having a reformatting zone including an object-accessible region and at least one object-excluding region. A portion of the carrier fluid may be moved from the object-accessible region to the at least one object-excluding region in an upstream section of the reformatting zone, to reduce a spacing of objects of the set. The portion of the carrier fluid may be directed into the object-accessible region from the at least one object-excluding region in a downstream section of the reformatting zone, to increase a spacing of objects of the set. The steps of moving and directing in combination may increase the spacing between objects disproportionately for a subset of the objects that are closest to one another.

Abstract: Provided herein are compositions and methods for generating phase-shift barcode oligonucleotides for library construction for next-generation sequencing. In some cases, barcode oligonucleotides are attached to particles or beads. Also provided are methods and kits for using the phase-shift barcode oligonucleotides in sequencing assays.

Abstract: The present invention relates generally to droplet creation, fusion and sorting, and incubation for droplet-based microfluidic assays. More particularly, the present invention relates to delay-lines, which allow incubation of reactions for precise time periods. More particularly, the present invention relates to delay lines for incubations up to three hours, while reducing back-pressure and dispersion in the incubation time due to the unequal speeds with which droplets pass through the delay line.