Generating spatial arrays with gradients

A method for identifying a location of an analyte in a biological sample, comprising:

• (a) exposing a biological sample to a concentration gradient of a first gradient-tagging oligonucleotide such that the first gradient-tagging oligonucleotide spatially tags the biological sample, wherein the concentration of the first gradient-tagging oligonucleotide varies at different locations in the biological sample ;
• (b) contacting the spatially-tagged biological sample with an array comprising a plurality of capture probes;
• (c) allowing the analyte present in the spatially-tagged biological sample to interact with a first capture probe of the plurality of capture probes present at a location on the array, wherein the first capture probe comprises a spatial barcode, and wherein the spatial barcode correlates with the location on the array;
• (d) allowing one or more first gradient-tagging oligonucleotides from the spatially-tagged biological sample to interact with one or more second capture probes of the plurality of capture probes present at the location on the array, wherein the number of the one or more first gradient-tagging oligonucleotides that interact(s) with the one or more second capture probes at the location on the array is correlated with a location within the biological sample;
• and
• (e) determining:
• the spatial barcode of the first capture probe that interacts with the analyte, and the number of the one or more first gradient-tagging oligonucleotides that interact with the one or more second capture probes at the location on the array, thereby identifying the location of the analyte in the biological sample.

A method for generating a spatial array, the method comprising:

• (a) providing an array comprising a plurality of immobilized oligonucleotides;
• (b) exposing the array to a concentration gradient of a first gradient-tagging oligonucleotide, wherein the concentration gradient of the first gradient-tagging oligonucleotide varies along a first direction of the array;
• (c) attaching one or more first gradient-tagging oligonucleotides to an immobilized oligonucleotide of the plurality of immobilized nucleotides to generate a tagged oligonucleotide, wherein the number of the one or more first gradient-tagging oligonucleotides attached to the tagged oligonucleotide correlates with a location along the first direction of the array;
• and
• (d) attaching a capture domain to the tagged oligonucleotide;
• thereby generating the spatial array.

A method, comprising:

• exposing an array of features on a substrate to N different gradient-tagging oligonucleotides and to bind at least one of the gradient-tagging oligonucleotides to at least one of the features of the array, so that different features in the array are bound to a different set of concentrations of the N different gradient-tagging oligonucleotides;
• for a feature in the array, determining a concentration of at least one of the N different gradient-tagging oligonucleotides bound to the feature;
• and
• identifying a location of the feature in the array based on the concentrations of the one or more of the N different gradient-tagging oligonucleotides bound to the feature,
• wherein N is greater than or equal to 2.