Spatial assays with perturbed cells

Abstract

This disclosure relates to methods for spatial profiling of analytes present in a biological sample. Also provided are methods for using spatially barcoded arrays to detect a biological analyte in a cell comprising a small molecule or exogenous analytes, including nucleic acids such as DNA or RNA and protein. Compostions using the methods also are disclosed.

What is claimed is: 
     
         1 . A method for determining the presence or abundance of a moiety in a cell comprising:
 (a) contacting the cell with an array comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises: (i) a spatial barcode and (ii) a capture domain, wherein the cell comprises the moiety and wherein the moiety comprises a moiety sequence;   (b) hybridizing a moiety sequence to the capture domain; and   (c) determining (i) all or a part of the sequence of the moiety sequence bound to the capture domain, or a complement thereof, and (ii) all or a part of the sequence of the spatial barcode, or a complement thereof, and using the determined sequence of (i) and (ii) to determine the presence or abundance of the moiety in the cell.