Abstract: The present disclosure relates to compositions and methods for tracking and spatially localizing a cell-expressed fusion protein within the cell (with the fusion protein optionally associated with a subcellular compartment, organelle, synapse, or the like), in a manner that minimizes any disruptive impact upon the cell, at least until the detection process is initiated. Use of transcriptomics and/or barcode nucleic acid detection is employed to assess both spatial localization of intracellularly tagged fusion proteins and to establish cell-cell connectivity, e.g., in neurons across a synapse, by associating axonal identities with individual neurons at the molecular tag and transcriptome level.

Abstract: The technology described herein provides tissue dissociation well plates, devices, systems, and kits to isolate single-cells or a single-nuclei using wells with roughened, angled bottom surfaces to receive pipette tips delivering tissue samples and isolation buffers. In certain examples, the bottom surfaces of the wells are roughened to aid in breaking down the tissue sample. In other examples, the tip of the pipette is roughened or serrated to aid in breaking down the tissue sample. The wells may be arrayed in a solid rigid upper surface. The pipette tips deliver isolation buffers and/or dissociation fluids to the wells and the tissue samples. The fluid delivery is provided by pumps via one or more perfusion manifolds. A pipette adaptor raises, lowers, and twists the pipette tips. The pipette tips deliver the dissociation fluid, withdraw the tissue samples with a suction force, and return the tissue samples to the well with an expelling force.

Abstract: Embodiments disclosed herein provide for spatially tagged nuclei that are compatible with any genomic or multiomic single cell/nuclei assay to allow generation of a spatially resolved single cell sequencing library with single cell resolution.

Abstract: Compositions and methods for assessing relative macromolecule abundance (for example, RNA expression levels) in a spatially-defined manner across a tissue sample (for example, from brain, lung, liver, kidney, pancreas, and/or heart) are disclosed, specifically providing deep transcriptomic coverage at high-resolution (for example, at approximate 10 ?m (single cell) resolution) across multiple locations assessed across the tissue sample

Abstract: Compositions and methods for assessing relative macromolecule abundance (for example, RNA expression levels) in a spatially-defined manner across a tissue sample (for example, from brain, lung, liver, kidney, pancreas, and/or heart) are disclosed, specifically providing deep transcriptomic coverage at high-resolution (for example, at approximate 10 ?m (single cell) resolution) across multiple locations assessed across the tissue sample.

Abstract: The present disclosure relates to compositions and methods for detecting nucleic acid sequences (e.g., coding and non-coding RNAs; nuclear/genomic DNA; mtDNA; pathogen nucleic acids, etc.) in a tissue sample, specifically providing improved matrices and matrix-employing methods for performance of nucleic acid capture and amplification in a tissue sample in situ and/or in a manner that retains spatial location information for captured nucleic acids (including nucleic acid-associated macromolecules).

Abstract: The present disclosure relates to compositions and methods for assessing relative DNA levels (e.g., levels of genomic DNA, mtDNA, viral DNA, bacterial DNA, etc.) in a spatially-defined manner across a tissue sample, specifically providing DNA sequence identity and relative abundance information at high-resolution across multiple locations assessed across the tissue sample.

Abstract: The present invention provides for methods of identifying cell types and cell subtypes from a biological sample or population of target cells. The methods further provide for determining cell type or cell subtype signatures. The method further provides for bipolar cell subtypes and markers and cell signatures thereof.

Abstract: The present disclosure relates to compositions and methods for assessing relative macromolecule abundance (e.g., RNA expression levels) in a spatially-defined manner across a tissue sample, specifically providing deep transcriptomic coverage at high-resolution across multiple locations assessed across the tissue sample.

Abstract: The present invention provides for methods of identifying cell types and cell subtypes from a biological sample or population of target cells. The methods further provide for determining cell type or cell subtype signatures. The method further provides for bipolar cell subtypes and markers and cell signatures thereof.