Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.

Abstract: Provided herein are methods of determining a location of an analyte in a biological sample, and systems for performing these methods. In particular, the methods and systems comprise decreasing the binding events of an analyte from a biological sample to capture probes that surround a biological sample positioned on a substrate.

Abstract: Provided herein are methods of identifying a location of an analyte in a biological sample using padlock oligonucleotides and rolling circle amplification. For example, provided herein are methods for identifying a location of an analyte in a biological sample where (i) a padlock oligonucleotide hybridizes to an analyte and is ligated thereby creating a circularized padlock oligonucleotide, (ii) rolling circle amplification of the circularized padlock oligonucleotide results in generation of an amplified circularized padlock oligonucleotide, and (iii) a signal corresponding to the amplified circularized padlock oligonucleotide is detected and used to identify the location of the analyte in the biological sample. Also provided are methods for identifying whether a treatment of a biological sample facilitates the release and subsequent detection of an analyte from the biological sample using padlock oligonucleotides and rolling circle amplification.

Abstract: In some aspects disclosed herein are methods and compositions for detecting an analyte such as a target nucleic acid in a biological sample, said method comprising generating and analyzing a detectable signal associated with the target nucleic acid and a separate signal associated with a region of interest in the target nucleic acid.

Abstract: In some aspects disclosed herein are methods and compositions for detecting analytes such as a plurality of nucleic acid molecules in a biological sample, said method comprising generating and analyzing a first detectable signal and a second detectable signal corresponding to a first target sequence and a second target sequence, respectively. The first and second target sequences can be present and/or expressed at different levels in the biological sample.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.

Abstract: Provided herein are methods, compositions, and kits, for capturing analytes from an embedded biological sample and spatially barcoding the analytes with an array.

Abstract: The present disclosure provides, among other things, methods, compositions and kits for analyzing the presence and location of nucleic acids with respect to analytes in a biological sample, for example by hybridization of amplified nucleic acid probes. In some aspects, the present disclosure provides a method of assessing the spatial or geographical distribution of RNA in a biological sample.

Abstract: An in vivo method of modifying a genome of a target cell in a mammalian subject is described. The method includes administering an effective amount of a transducer cell to the subject, where the transducer cell includes a regulated viral vector delivery system (RVVDS) for producing and releasing viral transduction particles (VTPs) when the transducer cell is exposed to inducing conditions, and each VTP comprises a nucleic acid encoding a genome modification system (GMS) comprising a genome modification protein and one or more elements that regulate expression or activity of the genome modification protein in a mammalian cell.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample.