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 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.