Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: A sample holder is provided. The sample holder includes a first member including a first retaining mechanism configured to retain a first substrate comprising a sample. The first retaining mechanism configured to retain the first substrate disposed in a first plane. The sample holder further includes a second member including a second retaining mechanism configured to retain a second substrate including a reagent medium disposed in a second plane. The sample holder further includes an alignment mechanism connected to one or both of the first member and the second member. The alignment mechanism configured to align the first and second members along the first plane and/or the second plane such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned and within a threshold distance along an axis orthogonal to the second plane.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: Provided herein are methods, compositions, and systems for improved in situ detection of analytes and spatial analysis using, e.g., a sequencing readout.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: A method for aligning a sample to an array is provided. An image of sample image of a sample can be received by a data processor. The sample image having a first resolution. An array image including an overlay of an array with the sample and an array fiducial can be received by the data processor. The array image having a second resolution lower than the first resolution of the sample image. The sample image can be registered to the array image by aligning the sample image and the array image. An aligned image can be generated based on the registering. The aligned image can include an overlay of the sample image with the array. The aligned image can be provided by the data processor. A method for detecting fiducials associated with an array is provided. Systems and non-transitory computer readable mediums performing the method are also provided.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: Provided herein are methods, compositions and systems for identifying spatial gene expression of analytes from glioblastoma derived tissue. The methods discloses herein include using templated ligation probe pairs to identify location of a disease proliferating region in a glioblastoma-derived sample by detecting analytes in the region and hybridizing a ligation product comprising the probe pairs to a capture probe on a spatial array.

Abstract: The present disclosure provides electrophoretic systems, methods and compositions for spatial analysis, which can serve to magnify or demagnify spatial resolution of analytes of interest that are captured using electrophoresis. Some implementations can use a diverging or converging electric field in an electrophoretic capture system. Such a divergent or convergent electric field, as opposed to a parallel electric field, can be generated by, for example, utilizing different sizes of electrodes associated with or imbedded in substrates. Also provided herein are electrophoretic systems, methods and compositions for spatial analysis, which can serve to selectively migrate one or more analytes from a region of interest in the biological sample for capture using electrophoresis.

Abstract: Provided herein are methods of enhancing spatial resolution of an analyte using sandwich maker system. The methods and systems used herein include a first substrate that includes a plurality of probes that include a capture domain and a spatial domain and a second substrate that includes a plurality of probes comprising a capture domain and a spatial domain.

Abstract: A method for aligning a sample to an array is provided. An image of sample image of a sample can be received by a data processor. The sample image having a first resolution. An array image including an overlay of an array with the sample and an array fiducial can be received by the data processor. The array image having a second resolution lower than the first resolution of the sample image. The sample image can be registered to the array image by aligning the sample image and the array image. An aligned image can be generated based on the registering. The aligned image can can include an overlay of the sample image with the array. The aligned image can be provided by the data processor. A method for detecting fiducials associated with an array is provided. Systems and non-transitory computer readable mediums performing the method are also provided.

Abstract: Disclosed herein are devices and methods for contacting a tissue sample with liquids to perform a variety of processes and analyses. In various embodiments, the device includes a hydrophilic flow path defined at least in part by a surface pattern (e.g., bounded by hydrophobic regions). The flow path includes a sample area sized to receive a biological sample. The flow path includes at least one valve configured to control flow in the flow path in response to an external stimulus.

Abstract: Provided herein are methods and systems for determining the location of one or more analytes in a biological sample with electrophoresis analyte transfer modes.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: Various implementations of electrophoretic systems and instruments are provided to improve electrophoresis and ease of use. Various electrophoretic systems and instruments utilize different electrode designs that can result in uniform electromigration of analytes. The electrophoretic systems and instrumentations optimize the size and/or location of electrodes relative to a sample, thereby increasing uniformity of electric field and reducing or minimizing drift of analyte migration. In addition, the electrophoresis systems and instruments provide a solution to conveniently check for electrical connections in the systems and instruments, and alert users of potential improper electrical connections, prior to performing electrophoresis.

Abstract: The present disclosure provides electrophoretic systems, methods and compositions for spatial analysis, which can serve to magnify or demagnify spatial resolution of analytes of interest that are captured using electrophoresis. Some implementations can use a diverging or converging electric field in an electrophoretic capture system. Such a divergent or convergent electric field, as opposed to a parallel electric field, can be generated by, for example, utilizing different sizes of electrodes associated with or imbedded in substrates. Also provided herein are electrophoretic systems, methods and compositions for spatial analysis, which can serve to selectively migrate one or more analytes from a region of interest in the biological sample for capture using electrophoresis.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: Quantitative methods for optimizing the permeabilization of cellular tissues for spatial transcriptomics are provided. Also provided is an instrument for quantitatively optimizing the permeabilization of cellular tissues used for spatial transcriptomics.