Abstract: The present disclosure provides methods, systems, compositions, and kits for analyzing target molecules, including using probes comprising a plurality of components for analyzing target molecules in situ in a sample.

Abstract: The present disclosure provides methods, systems and compositions for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix. The present disclosure also provides methods, systems and compositions for processing a biological sample for use in nucleic acid sequence detection.

Abstract: The present disclosure provides methods and systems for analyzing agents (e.g., therapeutic agents) in a biological sample having a three-dimensional matrix.

Abstract: The present disclosure provides methods and systems for generating indices in a synthetic three-dimensional (3D) matrix within a biological sample (e.g., a cell or a tissue sample). The present disclosure also provides methods and systems for using indices in the synthetic 3D matrix to index target molecules and for sequencing the target molecules in vitro.

Abstract: The present disclosure provides methods and systems for analyzing a biological sample from a subject, comprising using probes to identify and determine the location of different genetic sequences.

Abstract: Provided herein are methods and systems for transfer target molecules to a surface, such as a planar surface. The transferred target molecules can be used for downstream applications, such as sequence identification.

Abstract: The present disclosure provides methods, systems, compositions, and kits for analyzing target molecules, including using probes comprising a plurality of components for analyzing target molecules in situ in a sample.

Abstract: The present disclosure provides methods and systems for analyzing a biological sample from a subject, comprising using probes to identify and determine the location of different genetic sequences.

Abstract: The present disclosure provides methods and systems for generating and using indices in a synthetic three-dimensional (3D) matrix within a biological sample (e.g., a cell or a tissue sample). The present disclosure provides a method for processing or analyzing a nucleic acid molecule having a three-dimensional (3D) spatial position in a cell or cell derivative can comprise: (a) using a transposase to insert a nucleic acid index sequence into the nucleic acid molecule to generate an indexed nucleic acid molecule comprising the nucleic acid index sequence; (b) detecting the nucleic acid index sequence of the indexed nucleic acid molecule to identify the 3D spatial position; (c) subsequent to (b), removing the indexed nucleic acid molecule or derivative thereof from the 3D spatial position; and (d) identifying a sequence of the indexed nucleic acid molecule or derivative thereof removed from the 3D spatial position in (c).

Abstract: The present disclosure provides methods and systems for analyzing a biological sample from a subject, comprising using probes to identify and determine the location of different genetic sequences.

Abstract: The present disclosure provides methods, systems and compositions for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix.

Abstract: The present disclosure provides methods and systems for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix. The present disclosure also provides methods and systems for processing a biological sample for use in nucleic acid sequence detection.

Abstract: The present disclosure provides methods, systems, compositions, and kits for analyzing target molecules, including using probes comprising a plurality of components for analyzing target molecules in situ in a sample.

Abstract: The present disclosure provides methods and systems for determining the location and identity of variant sequences. The present disclosure also provides methods of treating diseases and of using spatial information of variant sequences in a biological sample to guide treatment selection in a corresponding subject.

Abstract: The present disclosure provides compositions and methods for making and using a support (e.g., a sample slide) for sample analysis. The present disclosure also provides compositions, methods, and systems for processing a sample on the support for use in nucleic acid sequence detection.

Abstract: The present disclosure provides methods and systems for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix. The present disclosure also provides methods and systems for processing a biological sample for use in nucleic acid sequence detection.

Abstract: Provided herein are compositions, methods, and systems for amplifying and identifying nucleic acids within a biological sample. The compositions, methods, and systems are generally compatible with volumetric imaging techniques and samples comprising nucleic acids contained within a three-dimensional matrix.

Abstract: The present disclosure provides methods and systems for analyzing agents (e.g., therapeutic agents) in a biological sample having a three-dimensional matrix.

Abstract: The present disclosure provides methods and systems for generating indices in a synthetic three-dimensional (3D) matrix within a biological sample (e.g., a cell or a tissue sample). The present disclosure also provides methods and systems for using indices in the synthetic 3D matrix to index target molecules and for sequencing the target molecules in vitro.

Abstract: Provided herein are methods and systems for transfer target molecules to a surface, such as a planar surface. The transferred target molecules can be used for downstream applications, such as sequence identification.