Compositions and methods for visualizing glycosylation

Abstract

In some aspects, provided herein are compositions and methods for imaging a sample by obtaining a profile of carbohydrates present in the sample. Also provided herein is a kit for imaging a sample to obtain a profile of carbohydrates present in the sample. Images obtained can be used in a computer implemented method disclosed herein for analyzing a sample.

Description

WSGR Docket No.: 42256-622.601 COMPOSITIONS AND METHODS FOR VISUALIZING GLYCOSYLATION CROSS-REFERENCE

[0001] The present application claims the benefit of U.S. Provisional Application No. 63 / 557,257, filed February 23, 2024, and U.S. Provisional Application No.63 / 729,747, filed December 9, 2024, each of which is entirely incorporated herein by reference. STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

[0002] This invention was made with government support under R00 NS120278 awarded by the National Institutes of Health. The government has certain rights in the invention. BACKGROUND

[0003] The process of glycosylation is a highly conserved molecular process by which carbohydrate moieties are added to proteins or lipids in order to modulate their overall structure and function. These modifications are critical molecular determinants of cellular function and can play key roles in signaling, cellular adhesion, protein folding, trafficking, or as a biomarker of disease. Glycosylation is also spatially regulated and disparate glycosylation patterns are found in various locations within the cell. Therefore, there is a need for methods of analysis of glycosylation in situ. SEQUENCE LISTING

[0004] The application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on February 11th, 2025, is named 42256-622.601_SL.xml, is 48,924 bytes in size, and is incorporated by reference as if written herein in its entirety. SUMMARY

[0005] Provided herein is a method of imaging a sample, the method comprising: (i) contacting the sample with (a) a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to an oligonucleotide; and (b) a subset of a plurality of fluorescently labeled nucleic acid probes, wherein each nucleic acid probe specifically binds to only one of the oligonucleotides of (i)(a), thereby generating a probe / carbohydrate binding protein complex; (ii) imaging the sample to detect a binding of each of the probe / carbohydrate binding protein complexes of step (i)(b); and (iii) removing the probes bound to the carbohydrate binding proteins in step (i)(b), wherein the carbohydrate binding proteins remain bound to the sample.WSGR Docket No.: 42256-622.601

[0006] In some embodiments, the method further comprises repeating steps (i) to (iii) with a different subset of the plurality of fluorescently labeled nucleic acid probes of (i)(b) until all subsets of the plurality of fluorescently labeled nucleic acid probes have been utilized.

[0007] In some embodiments, the plurality of carbohydrate binding proteins comprises a lectin.

[0008] In some embodiments, the plurality of carbohydrate binding proteins comprises a mannose-binding protein.

[0009] In some embodiments, the plurality of carbohydrate binding proteins comprises a catalytically inactivated enzyme.

[0010] In some embodiments, the catalytically inactive enzyme is a glycosylase.

[0011] In some embodiments, the catalytically inactive enzyme is a transferase.

[0012] In some embodiments, the catalytically inactive enzyme is inactivated by one or more mutations.

[0013] In some embodiments, the catalytically inactive enzyme is inactivated by truncation.

[0014] In some embodiments, the plurality of carbohydrate binding proteins comprises about 5, about 10, about 15, about 20, about 25, about 30, about 35, or about 40 different carbohydrate binding proteins.

[0015] In some embodiments, the plurality of carbohydrate binding proteins comprises two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.

[0016] In some embodiments, the plurality of carbohydrate binding proteins comprises a recombinant protein.

[0017] In some embodiments, the carbohydrate binding protein is covalently bound to the oligonucleotide via a copper-free click chemistry reaction.

[0018] In some embodiments, each carbohydrate binding protein of the plurality of carbohydrate binding proteins is covalently bound to from 1 to about 15 copies of the oligonucleotide.

[0019] In some embodiments, the sample comprises a whole tissue.

[0020] In some embodiments, the sample comprises a tissue section.

[0021] In some embodiments, the sample is obtained from muscle, brain, a nerve, a sciatic nerve, spinal cord, kidney, liver, heart, lung, lymph node, spleen, or intestine tissue.

[0022] In some embodiments, the sample is fixed.

[0023] In some embodiments, the sample is not fixed.

[0024] In some embodiments, step (iii) comprises contacting the sample with dimethyl sulfoxide (DMSO) or formamide.

[0025] In some embodiments, the plurality of carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having at least 80% sequence identity to a sequence ofWSGR Docket No.: 42256-622.601 SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 36; xxxi)WSGR Docket No.: 42256-622.601 UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 55.

[0026] In some embodiments, the plurality of carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to anWSGR Docket No.: 42256-622.601 oligonucleotide having a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having a sequence of SEQ ID NO: 55.

[0027] Also provided herein is a method of imaging a sample, the method comprising: (i) contacting the sample with a plurality of different carbohydrate binding proteins, wherein each different carbohydrate binding protein of the plurality of different carbohydrate binding proteins is covalently bound to a barcode oligonucleotide of a plurality of barcode oligonucleotides, wherein, upon the contacting, a subset of the plurality of different carbohydrate binding proteinsWSGR Docket No.: 42256-622.601 binds to the sample; (ii) contacting the sample with a plurality of fluorescently labeled first nucleic acid probes, wherein each fluorescently labeled first nucleic acid probe of the plurality of fluorescently labeled first nucleic acid probes binds to a first barcode oligonucleotide of the plurality of barcode oligonucleotides of step (i), thereby generating a first binary complex of the fluorescently labeled first nucleic acid probe / first barcode oligonucleotide; (iii) imaging the sample to detect a presence or absence of the first binary complex of step (ii); and (iv) removing the plurality of fluorescently labeled first nucleic acid probes from the sample, wherein the subset of the plurality of different carbohydrate binding proteins remain bound to the sample.

[0028] In some embodiments, the method further comprises: (ii’) contacting the sample with a plurality of fluorescently labeled second nucleic acid probes, wherein each fluorescently labeled second nucleic acid probe of the plurality of fluorescently labeled second nucleic acid probes is configured to bind to a second barcode oligonucleotide of the plurality of barcode oligonucleotides of step (i), thereby generating a second binary complex of the fluorescently labeled second nucleic acid probe / second barcode oligonucleotide; (iii’) imaging the sample to detect a presence or absence of the second binary complex of step (ii’); and (iv’) removing the plurality of fluorescently labeled second nucleic acid probes from the sample, wherein the subset of the plurality of different carbohydrate binding proteins remain bound to the sample.

[0029] In some embodiments, the method further comprises repeating steps (ii) to (iv) multiple times, each time with a plurality of fluorescently labeled additional nucleic acid probes, wherein each fluorescently labeled additional nucleic acid probe of the plurality of fluorescently labeled additional nucleic acid probes is configured to bind to an additional barcode oligonucleotide of the plurality of barcode oligonucleotides of step (i).

[0030] In some embodiments, the imaging comprises measuring a staining intensity.

[0031] In some embodiments, the plurality of different carbohydrate binding proteins comprises one or more lectins.

[0032] In some embodiments, the plurality of different carbohydrate binding proteins comprises one or more mannose-binding proteins.

[0033] In some embodiments, the plurality of different carbohydrate binding protein comprises one or more catalytically inactivated enzymes.

[0034] In some embodiments, the one or more catalytically inactive enzymes comprise a glycosylase.

[0035] In some embodiments, the one or more catalytically inactive enzymes comprise a transferase.

[0036] In some embodiments, the one or more catalytically inactive enzymes comprise an enzyme inactivated by one or more mutations.WSGR Docket No.: 42256-622.601

[0037] In some embodiments, the one or more catalytically inactive enzymes comprise an enzyme inactivated by truncation.

[0038] In some embodiments, the plurality of different carbohydrate binding proteins comprises about 5, about 10, about 15, about 20, about 25, about 30, about 35, or about 40 different carbohydrate binding proteins.

[0039] In some embodiments, the plurality of different carbohydrate binding proteins comprises two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.

[0040] In some embodiments, the plurality of different carbohydrate binding protein comprises a recombinant protein.

[0041] In some embodiments, each carbohydrate binding protein of the plurality of different carbohydrate binding proteins is covalently bound to the barcode oligonucleotide via a copper- free click chemistry reaction.

[0042] In some embodiments, each different carbohydrate binding protein of the plurality of different carbohydrate binding proteins is covalently bound to from 1 to about 15 copies of the barcode oligonucleotide.

[0043] In some embodiments, the sample comprises a whole tissue.

[0044] In some embodiments, the sample comprises a tissue section.

[0045] In some embodiments, the sample is obtained from muscle, brain, a nerve, a sciatic nerve, spinal cord, kidney, liver, heart, lung, lymph node, spleen, or intestine tissue.

[0046] In some embodiments, the sample is fixed.

[0047] In some embodiments, the sample is not fixed.

[0048] In some embodiments, step (iv) comprises contacting the sample with DMSO or formamide.

[0049] In some embodiments, the plurality of different carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having at least 80%WSGR Docket No.: 42256-622.601 sequence identity to a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotideWSGR Docket No.: 42256-622.601 having at least 80% sequence identity to a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 55.

[0050] In some embodiments, the plurality of different carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotideWSGR Docket No.: 42256-622.601 having a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having a sequence of SEQ ID NO: 55.

[0051] Also provided herein is a composition comprising a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to an oligonucleotide, and wherein the oligonucleotide comprises a sequence having at least 80% identity to a sequence set forth in any one of SEQ ID NOs: 1-55.

[0052] In some embodiments, the oligonucleotide comprises a sequence set forth in any one of SEQ ID NOs: 1-55.

[0053] Also provided herein is a composition comprising: (i) a sample comprising cells embedded onto a planar surface; (ii) a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to a different oligonucleotide; and (iii) a plurality of fluorescently labeled nucleic acid probes, wherein each nucleic acid probe specially binds to only one of the oligonucleotides;

[0054] In some embodiments, the plurality of carbohydrate binding proteins comprises a lectin.

[0055] In some embodiments, the plurality of carbohydrate binding proteins comprises a mannose-binding protein.WSGR Docket No.: 42256-622.601

[0056] In some embodiments, the plurality of carbohydrate binding proteins comprises a catalytically inactivated enzyme.

[0057] In some embodiments, the catalytically inactive enzyme is a glycosylase.

[0058] In some embodiments, the catalytically inactive enzyme is a transferase.

[0059] In some embodiments, the catalytically inactive enzyme is inactivated by one or more mutations.

[0060] In some embodiments, the catalytically inactive enzyme is inactivated by truncation.

[0061] In some embodiments, the plurality of carbohydrate binding proteins comprises a carbohydrate binding protein listed in Table 1 or Table 3, or two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.

[0062] In some embodiments, the plurality of carbohydrate binding proteins comprises two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotideWSGR Docket No.: 42256-622.601 having at least 80% sequence identity to a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 55.WSGR Docket No.: 42256-622.601

[0063] In some embodiments, the plurality of carbohydrate binding proteins comprises two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotideWSGR Docket No.: 42256-622.601 having a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having a sequence of SEQ ID NO: 55.

[0064] Also provided herein is a kit comprising: (iii) a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to a different oligonucleotide; (ii) a plurality of fluorescently labeled nucleic acid probes, wherein each nucleic acid probe is configured to specifically bind to only one of the oligonucleotides of step (i); and (iii) a denaturing agent capable of removing a nucleic acid probe that is bound to an oligonucleotide-bound-carbohydrate binding protein.

[0065] In some embodiments, the plurality of carbohydrate binding proteins comprises a carbohydrate binding protein listed in Table 1 or Table 3, or two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.

[0066] In some embodiments, the plurality of carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having at least 80% sequenceWSGR Docket No.: 42256-622.601 identity to a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having at least 80%WSGR Docket No.: 42256-622.601 sequence identity to a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 55.

[0067] In some embodiments, the plurality of carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotideWSGR Docket No.: 42256-622.601 having a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having a sequence of SEQ ID NO: 55.

[0068] Also provided herein is a method of conjugating a carbohydrate binding protein to an oligonucleotide, the method comprising: (i) contacting the carbohydrate binding protein with dibenzocyclooctyne (DBCO) comprising a tetrafluorophenyl ester group, thereby generating a DBCO-labeled carbohydrate binding protein; and (ii) contacting the DBCO-labeled carbohydrate binding protein with an oligonucleotide, wherein the oligonucleotide is conjugated to an azide moiety; thereby conjugating the carbohydrate binding protein to the oligonucleotide.

[0069] In some embodiments, the oligonucleotide comprises sequence having at least 80% identity to a sequence set forth in any one of SEQ ID NOs: 1-55.

[0070] In some embodiments, the oligonucleotide comprises sequence set forth in any one of SEQ ID NOs: 1-55.

[0071] In some embodiments, the carbohydrate binding protein is selected from the carbohydrate binding proteins listed in Table 1 or Table 3.

[0072] Also provided herein is a computer implemented method for analyzing a sample, the method comprising: (i) receiving input comprising images of the sample, wherein the images of the sample comprise images generated by the method of any one of the preceding embodiments; and (ii) generating, using a machine learning algorithm, an output comprising a quantitative or qualitative value of functional or structural features of the sample.

[0073] Also provided herein is a method of detecting a tissue pathology, the method comprising: (i) obtaining a tissue sample; and (ii) applying the method of any one of the preceding embodiments to the tissue sample.WSGR Docket No.: 42256-622.601

[0074] In some embodiments, the tissue sample comprises cancer cells.

[0075] In some embodiments, the tissue sample comprises cells comprising a disorder of glycosylation.

[0076] In some embodiments, the tissue sample comprises a glycosylation pattern that is different from a tissue sample that does not comprise cancer cells or cells comprising a disorder of glycosylation.

[0077] In some embodiments, the tissue sample comprises a lower or higher expression level of the fluorescently labeled nucleic acid probes of any one of the preceding embodiments.

[0078] In some embodiments, the disorder of glycosylation comprises Saul-Wilson Syndrome (SWS) or GNE myopathy.

[0079] In some embodiments, the cancer is pancreatic ductal adenocarcinoma (PDAC).

[0080] Also provided herein is a method of characterizing a cancer in a subject, the method comprising: (i) obtaining a tissue sample from the subject, wherein the tissue sample comprises a cancer tissue; and (ii) applying the method of any one of the preceding embodiments to the tissue sample.

[0081] In some embodiments, the cancer is pancreatic ductal adenocarcinoma (PDAC).

[0082] In some embodiments, the characterizing comprises identifying a border between the cancer tissue and a healthy tissue in the tissue sample.

[0083] In some embodiments, the border is identified by detecting a lower or higher expression level of the fluorescently labeled nucleic acid probes of any one of the preceding embodiments by the cancer tissue compared to the healthy tissue.

[0084] In some embodiments, the characterizing comprises determining a size of a tumor.

[0085] In some embodiments, the characterizing comprises determining progression of the tumor.

[0086] In some embodiments, the progression is measured by comparing results obtained from a first tissue sample to results obtained from a second tissue sample, wherein the second tissue sample is obtained at least one week later than the first tissue sample. INCORPORATION BY REFERENCE

[0087] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. BRIEF DESCRIPTION OF THE DRAWINGS

[0088] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will beWSGR Docket No.: 42256-622.601 obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:

[0089] FIGs.1A-1C depict results measuring conjugation of dibenzocyclooctyne (DBCO) to IgG antibodies. FIG.1A depicts number of DBCO molecules per antibody when reacted with various concentrations of DBCO. FIG.1B depicts fluorescence microscopy images detecting antibodies conjugated with an optimal concentration of DBCO (middle), the limit of detection (left), or at saturation (right). FIG.1C is a quantification of the fluorescence intensity across the stained tissue.

[0090] FIG.2 depicts results measuring number of DBCO molecules per carbohydrate binding protein Wheat Germ Agglutinin (WGA) when reacted with various concentrations of DBCO.

[0091] FIG.3A is a fluorescence microscopy image of a skeletal muscle sample obtained using oligonucleotide-conjugated carbohydrate binding proteins bound to fluorescent oligonucleotide probes.

[0092] FIG.3B is a fluorescence microscopy image of a skeletal muscle sample obtained using oligonucleotide-conjugated antibodies bound to fluorescent oligonucleotide probes.

[0093] FIGs.4A-4E are fluorescence microscopy images detecting staining with carbohydrate binding proteins in a variety of cellular locations in a skeletal muscle sample. FIG.4A depicts nuclear staining; FIG.4B depicts peri-nuclear staining; FIG.4C depicts cytoplasmic staining; FIG.4D depicts cell membrane staining; and FIG.4E depicts extracellular matrix (ECM) staining.

[0094] FIGs.5A-5B are fluorescence microscopy image of a skeletal muscle sample obtained using carbohydrate binding proteins specific for certain cell types or tissue structures. FIG.5A depicts muscle fiber (LCA) and NMJ (VVL) staining. FIG.5B depicts staining of vessels (DSL), muscle spindles (PHAE), and motor nerves (ECL).

[0095] FIG.6 is a schematic diagram depicting a process by which a glycan profile is obtained for a skeletal muscle tissue sample and the resulting images are used to train an artificial intelligence algorithm to analyze structural features of the tissue.

[0096] FIGs.7A-7C depict examples of data output from an analysis performed by an artificial intelligence algorithm analyzing various parameters of skeletal muscle structure and function. FIG.7A depicts the capillary count; FIG.7B depicts the myofiber count; FIG.7C depicts the myofiber size.

[0097] FIGs.8A-8C are fluorescence microscopy images measuring glycan profiles in healthy (FIG.8A), denervated (FIG.8B), and regenerating (FIG.8C) skeletal muscle.WSGR Docket No.: 42256-622.601

[0098] FIG.9 is a schematic diagram depicting method of obtaining a glycan profile by staining a sample with a variety of carbohydrate binding proteins conjugated to oligonucleotides and obtaining serial images by staining with oligonucleotides complementary to a subset of the bound oligonucleotide-conjugated carbohydrate binding proteins. The resultant images can be used to resolve distributions of individual glycan moieties.

[0099] FIG.10A is a schematic diagram depicting a method of obtaining a glycan profile by staining a sample with a glycosylation landscape analysis by probe hybridization (GLYPH) panel of barcoded carbohydrate binding proteins including lectins, antibodies, and peptides. Carbohydrate binding proteins are conjugated with oligonucleotide barcodes using CLICK- chemistry and rendered via annealing with fluorescent cDNA probes. After imaging, probes are denatured and washed before the next cycle of imaging. Images are processed and aligned to generate GLYPH maps.

[0100] FIG.10B is a schematic diagram depicting a computational analysis of the profile obtained in FIG.10A by signal decomposition of mixed signals using known binding kinetics of carbohydrate binding proteins into individual glycan moieties. Cells and tissue structures are segmented, glycan signals are quantified for each cell, and analyzed for spatial relationships and enriched interactions.

[0101] FIG.11 depicts fluorescence microscopy images detecting glycosylation patterns of induced pluripotent stem cell (iPSC)-derived osteo-chondral organoids comparing organoids obtained from healthy iPSCs to those obtained from iPSCs carrying Saul-Wilson Syndrome mutations.

[0102] FIG.12 depicts a fluorescence microscopy image detecting glycosylation patterns of pancreatic ductal adenocarcinoma tissue samples comparing healthy tissue with tumor tissue.

[0103] FIG.13 depicts fluorescence microscopy images detecting glycosylation patterns of human muscle tissue comparing control samples to samples obtained from patients with GNE myopathy. DETAILED DESCRIPTION

[0104] While preferred embodiments of the present disclosure have been shown and described herein, it will be apparent to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and thatWSGR Docket No.: 42256-622.601 methods and structures within the scope of these claims and their equivalents be covered thereby.

[0105] Co-detection by indexing (CODEX) generally uses deoxyribonucleic acid (DNA)- conjugated antibodies and the cyclic addition and removal of complementary fluorescently labeled DNA probes to simultaneously visualize many markers in situ. CODEX enables a deep view into the single-cell spatial relationships in tissues and is intended to spur discovery in developmental biology, disease and therapeutic design. Glycosylation landscape analysis by probe hybridization (GLYPH) generally uses DNA-conjugated carbohydrate binding proteins and the cyclic addition and removal of complementary fluorescently labeled DNA probes to simultaneously visualize many markers in situ. GLYPH enables an unbiased, high resolution spatial analysis of patterns of glycosylation and may depict how these patterns contribute to biological functions and cellular responses in healthy or diseased tissues. The present disclosure allows for multiplexed spatial glycan profiling using DNA barcoding and iterative rendering to visualize and study glycosylation in situ. The results may provide combinatorial glycan profiles for specific cell types and / or tissue structures that can provide insights into disease, aging, and development. Certain Definitions

[0106] All terms are intended to be understood as they would be understood by a person skilled in the art. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the disclosure pertains.

[0107] Reference in the specification to “some embodiments,” “an embodiment,” “one embodiment” or “other embodiments” means that a feature, structure, or characteristic described in connection with the embodiments is included in at least some embodiments, but not necessarily all embodiments, of the present disclosure.

[0108] As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method or composition of the disclosure, and vice versa. Furthermore, compositions of the disclosure can be used to achieve methods of the disclosure.

[0109] Whenever the term “at least,” “greater than,” or “greater than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “at least,” “greaterWSGR Docket No.: 42256-622.601 than” or “greater than or equal to” applies to each of the numerical values in that series of numerical values. For example, greater than or equal to 1, 2, or 3 is equivalent to greater than or equal to 1, greater than or equal to 2, or greater than or equal to 3.

[0110] Whenever the term “no more than,” “less than,” or “less than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “no more than,” “less than,” or “less than or equal to” applies to each of the numerical values in that series of numerical values. For example, less than or equal to 3, 2, or 1 is equivalent to less than or equal to 3, less than or equal to 2, or less than or equal to 1.

[0111] Certain inventive embodiments herein contemplate numerical ranges. When ranges are present, the ranges include the range endpoints. Additionally, every sub range and value within the range is present as if explicitly written out. The term “about” or “approximately” may mean within an acceptable error range for the particular value, which will depend in part on how the value is measured or determined, e.g., the limitations of the measurement system. For example, “about” may mean within 1 or more than 1 standard deviation, per the practice in the art. Alternatively, “about” may mean a range of up to 20%, up to 10%, up to 5%, or up to 1% of a given value. Where particular values are described in the application and claims, unless otherwise stated the term “about” meaning within an acceptable error range for the particular value may be assumed.

[0112] As used herein, the terms “DNA barcoding,” “barcode,” or “barcode oligonucleotide” generally refer to a unique molecular tag / label that identifies the carbohydrate binding proteins to which the unique molecular tag / label is covalently bound. The length of the barcode can be from about 10 nucleic acids to about 20 nucleic acids, from about 20 nucleic acids to about 30 nucleic acids, or from about 30 nucleic acids to about 40 nucleic acids. The nucleic acid sequence of the barcode oligonucleotide can be determined, thereby identifying the carbohydrate binding proteins to which the barcode oligonucleotide is covalently bound. Methods of Imaging a Sample

[0113] In some aspects, the present disclosure provides a method of imaging a sample. In some embodiments, the method comprises contacting the sample with (i) a plurality of carbohydrate- binding proteins, wherein each carbohydrate-binding protein is covalently bound to an oligonucleotide and (ii) a subset of a corresponding plurality of fluorescently labeled nucleic acid probes, wherein each nucleic acid probe specifically binds to only one of the oligonucleotides covalently bound to each carbohydrate-binding protein, thereby generating a probe / carbohydrate-binding protein complex.

[0114] In some embodiments, the plurality of carbohydrate-binding proteins binds or couples to the sample. In some embodiments, the plurality of carbohydrate-binding proteins is coupled to aWSGR Docket No.: 42256-622.601 plurality of oligonucleotides. In some embodiments, a carbohydrate-binding protein of the plurality of carbohydrate-binding proteins is coupled to an oligonucleotide of the plurality of oligonucleotides. In some embodiments, a carbohydrate-binding protein of the plurality of carbohydrate-binding proteins is covalently bound to an oligonucleotide of the plurality of oligonucleotides. In some embodiments, a first subset of the plurality of carbohydrate-binding protein is coupled to a first subset of the plurality of oligonucleotides. In some embodiments, a second subset of the plurality of carbohydrate-binding proteins is coupled to a second subset of the plurality of oligonucleotides. In some embodiments, the first subset and the second subset of the plurality of carbohydrate-binding proteins are different. In some embodiments, the first subset and the second subset of the plurality of carbohydrate-binding proteins are same. In some embodiments, the first subset and the second subset of the plurality of oligonucleotides are same. In some embodiments, each carbohydrate-binding protein is covalently bound to a different oligonucleotide.

[0115] In some embodiments, the method further comprises contacting the sample with one or more fluorescently labeled nucleic acid probes (or probes, used interchangeably herein). In some embodiments, a fluorescently labeled nucleic acid probe binds or couples to an oligonucleotide. In some embodiments, the probe is selected from a subset of a corresponding plurality of fluorescently labeled nucleic acid probes. In some embodiments, a nucleic acid probe specifically binds to an oligonucleotide that is covalently bound to a carbohydrate-binding protein, thereby generating a probe / carbohydrate-binding protein complex (or probe / protein complex). In some embodiments, the method comprises contacting the sample with a subset of fluorescently labeled nucleic acid probes.

[0116] In some embodiments, the method further comprises imaging the sample to detect the binding of each of the probe / carbohydrate-binding protein complexes. In some embodiments, the method further comprises removing the probes bound to the carbohydrate-binding protein. In some embodiments, the method comprises repeating the foregoing steps with a different subset of fluorescently labeled nucleic acid probes until all subsets have been utilized.

[0117] In some embodiments, imaging comprises capturing an image. In some embodiments, capturing an image is performed by a method of microscopy. In some embodiments, the method of microscopy is fluorescence microscopy. In some embodiments, the method of microscopy is light microscopy. In some embodiments, the method of microscopy is confocal microscopy. In some embodiments, the method of microscopy is light sheet microscopy. In some embodiments, the method of microscopy is two-photon microscopy.

[0118] In some embodiments, the images captured using the methods described herein can provide information regarding the levels of glycosylation in the sample. In some embodiments,WSGR Docket No.: 42256-622.601 the images captured using the methods described herein can provide information regarding the location of glycosylation in the sample.

[0119] In some embodiments, the carbohydrate binding protein is a lectin. In some embodiments, the carbohydrate binding protein is a mannose-binding protein. In some embodiments, the carbohydrate binding protein is an enzyme. In some embodiments, the carbohydrate binding protein is a catalytically inactivated enzyme. In some embodiments, the catalytically inactivated enzyme is a glycosylase. In some embodiments, the catalytically inactivated enzyme is a transferase. In some embodiments, the catalytically inactivated enzyme is a lipase. In some embodiments, the catalytically inactivated enzyme is a polymerase. In some embodiments, the catalytically inactivated enzyme is a ligase. In some embodiments, the catalytically inactivated enzyme is a protease. In some embodiments, the catalytically inactivated enzyme is a hydrolase. In some embodiments, the catalytically inactivated enzyme is an oxidase. In some embodiments, the catalytically inactivated enzyme is a reductase. In some embodiments, the catalytically inactivated enzyme is an isomerase. In some embodiments, the catalytically inactivated enzyme is inactivated by one or more mutations, comprising one or more of: point mutations (e.g., missense, nonsense, silent), insertion / deletion mutations, and / or frameshift mutations. In some embodiments, the catalytically inactivated enzyme is inactivated by truncation.

[0120] In some embodiments, the plurality of carbohydrate binding proteins comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, or at least 50 different carbohydrate binding proteins. In some embodiments, the plurality of carbohydrate binding proteins comprises about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, or about 50 different carbohydrate binding proteins. In some embodiments, the plurality of carbohydrate binding proteins comprises a carbohydrate binding protein listed in Table 1 or Table 3, or two or more of the carbohydrate binding proteins listed in Table 1 or in Table 3.WSGR Docket No.: 42256-622.601 Table 1. Exemplary Carbohydrate Binding ProteinsWSGR Docket No.: 42256-622.601WSGR Docket No.: 42256-622.601WSGR Docket No.: 42256-622.601

[0121] In some embodiments, the carbohydrate binding protein comprises a carbohydrate binding protein with an amino acid or nucleic acid sequence having at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99%, or 100% sequence identity to a sequence of a carbohydrate binding protein of Table 1 or Table 3.

[0122] In some embodiments, the carbohydrate binding protein comprises a recombinant protein. In some embodiments, the carbohydrate binding protein comprises a non-recombinant protein.

[0123] In some embodiments, the carbohydrate binding protein is covalently bound to the oligonucleotide. In some embodiments, the carbohydrate binding protein is covalently bound to the oligonucleotide via a click chemistry reaction. In some embodiments, the carbohydrate binding protein is covalently bound to the oligonucleotide via a copper-free click chemistry reaction. In some embodiments, each carbohydrate binding protein is covalently bound to from 1 to about 30 copies, 1 to about 25 copies, 1 to about 20 copies, 1 to about 15 copies, 1 to about 10 copies, or 1 to about 5 copies of the oligonucleotide.

[0124] In some embodiments, the sample comprises a whole tissue. In some embodiments, the sample comprises at least a portion of a tissue. In some embodiments, the sample comprises a tissue section. In some embodiments, the tissue is obtained from muscle. In some embodiments, the sample is obtained from skeletal muscle. In some embodiments, the sample is obtained from smooth muscle. In some embodiments, the sample is obtained from cardiac muscle. In some embodiments, the sample is obtained from brain. In some embodiments, the sample is obtained from a nerve. In some embodiments, the tissue is obtained from a sciatic nerve. In some embodiments, the sample is obtained from spinal cord. In some embodiments, the sample is obtained from kidney. In some embodiments, the sample is obtained from liver. In some embodiments, the sample is obtained from lung. In some embodiments, the sample is obtainedWSGR Docket No.: 42256-622.601 from lymph node. In some embodiments, the sample is obtained from spleen. In some embodiments, the sample is obtained from intestine. In some embodiments, the sample is obtained from skin. In some embodiments, the sample is obtained from eye. In some embodiments, the sample is obtained from bone. In some embodiments, the sample is obtained from a tumor. In some embodiments, the sample is obtained from a solid tumor. In some embodiments, the sample is fixed. In some embodiments, the sample is not fixed.

[0125] In some embodiments, removing the probes bound to the carbohydrate binding proteins or the oligonucleotides that is bound to the carbohydrate binding proteins comprises contacting the sample with dimethyl sulfoxide (DMSO) or formamide at concentrations sufficient to denature the probes from the carbohydrate binding proteins or the oligonucleotides. In some embodiments, the sample is contacted with a 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 65%, 70%, 80%, or 90% solution of DMSO or formamide. In some embodiments, removing the probes bound to the carbohydrate binding proteins or the oligonucleotides comprises contacting the sample with an acidic solution such as, but not limited to, hydrochloric acid or acetic acid. In some embodiments, removing the probes bound to the carbohydrate binding proteins or the oligonucleotides comprises contacting the sample with a basic solution, such as, but not limited to, sodium hydroxide, calcium hydroxide, or potassium hydroxide.

[0126] Also provided herein is a method of imaging a sample. In some embodiments, the method comprises contacting the sample with a plurality of different carbohydrate binding proteins. In some embodiments, each different carbohydrate binding protein of the plurality of different carbohydrate binding proteins is covalently bound to a barcode oligonucleotide of a plurality of barcode oligonucleotides. In some embodiments, a subset of the plurality of different carbohydrate binding proteins is further bound to the sample. In some embodiments, the method further comprises contacting the sample with a plurality of fluorescently labeled first nucleic acid probes. In some embodiments, each fluorescently labeled first nucleic acid probe of the plurality of fluorescently labeled first nucleic acid probes is further configured to bind to a first barcode oligonucleotide of the plurality of barcode oligonucleotides. In some embodiments, this binding generates a first binary complex of the fluorescently labeled first nucleic acid probe / first barcode oligonucleotide. In some embodiments, the method further comprises imaging the sample to detect a presence or absence of the first binary complex. In some embodiments, the method further comprises removing the plurality of fluorescently labeled first nucleic acid probes from the sample, wherein the subset of the plurality of different carbohydrate binding proteins remain bound to the sample.

[0127] In some embodiments, the method further comprises contacting the sample with a plurality of fluorescently labeled second nucleic acid probes. In some embodiments, eachWSGR Docket No.: 42256-622.601 fluorescently labeled second nucleic acid probe of the plurality of fluorescently labeled second nucleic acid probes is configured to bind to a second barcode oligonucleotide of the plurality of barcode oligonucleotides. In some embodiments, this binding generates a second binary complex of the fluorescently labeled second nucleic acid probe / second barcode oligonucleotide. In some embodiments, the method further comprises imaging the sample to detect a presence or absence of the second binary complex. In some embodiments, the method further comprises removing the plurality of fluorescently labeled second nucleic acid probes from the sample, wherein the subset of the plurality of different carbohydrate binding proteins remain bound to the sample.

[0128] In some embodiments, the method comprises repeating contacting the sample with a plurality of fluorescently labeled nucleic acid probes. In some embodiments, the method further comprises imaging the sample to detect a presence or absence of the binary complex. In some embodiments, the method further comprises removing the plurality of fluorescently labeled nucleic acid probes from the sample. In some embodiments, the subset of the plurality of different carbohydrate binding proteins remain bound to the sample multiple times, each time with a plurality of fluorescently labeled additional nucleic acid probes. In some embodiments, each fluorescently labeled additional nucleic acid probe of the plurality of fluorescently labeled additional nucleic acid probes is configured to bind to an additional barcode oligonucleotide of the plurality of barcode oligonucleotides.

[0129] In some embodiments, imaging comprises measuring a staining intensity. In some embodiments, the staining intensity can be used to quantify the relative number of carbohydrate binding proteins bound to an area of the sample. In some embodiments, the plurality of different carbohydrate binding proteins comprises one or more lectins. In some embodiments, the plurality of different carbohydrate binding proteins comprises one or more mannose-binding proteins. In some embodiments, the plurality of different carbohydrate binding protein comprises one or more catalytically inactivated enzymes. In some embodiments, the one or more catalytically inactive enzymes comprise a glycosylase. In some embodiments, the one or more catalytically inactive enzymes comprises a transferase. In some embodiments, the one or more catalytically inactive enzymes comprise an enzyme inactivated by one or more mutations. In some embodiments, the one or more catalytically inactive enzymes comprise an enzyme inactivated by truncation. In some embodiments, the plurality of different carbohydrate binding proteins comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at leastWSGR Docket No.: 42256-622.601 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, or at least 50 different carbohydrate binding proteins. In some embodiments, the plurality of different carbohydrate binding proteins comprises about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, or about 50 different carbohydrate binding proteins. In some embodiments, the plurality of different carbohydrate binding proteins comprises two or more of the carbohydrate binding proteins listed in Table 1 or Table 3. In some embodiments, the plurality of different carbohydrate binding protein comprises a recombinant protein.

[0130] In some embodiments, the carbohydrate binding protein is covalently bound to the barcode oligonucleotide via a copper-free click chemistry reaction. In some embodiments, each different carbohydrate binding protein is covalently bound to from 1 to about 15 copies of the barcode oligonucleotide. In some embodiments, each carbohydrate binding protein is covalently bound to from 1 to about 30 copies, 1 to about 25 copies, 1 to about 20 copies, 1 to about 15 copies, 1 to about 10 copies, or 1 to about 5 copies of the barcode oligonucleotide.

[0131] In some embodiments, the oligonucleotide (or barcode oligonucleotide) comprises a sequence having at least 60%, at least 70%, at least 80%, at least 90%, or 100% identity to a sequence set forth in any one of SEQ ID NOs: 1-55 as shown in Table 2. In some embodiments, each of the carbohydrate binding proteins are conjugated to an oligonucleotide with at least 60%, at least 70%, at least 80%, at least 90%, or 100% sequence identity to any one of oligonucleotides as shown in Table 2. In some embodiments, each of the carbohydrate binding proteins are conjugated to an oligonucleotide as shown in Table 3. Compositions of Carbohydrate Binding Protein

[0132] Also provided herein is a composition comprising a plurality of carbohydrate binding proteins. In some embodiments, each carbohydrate binding protein of the plurality of carbohydrate binding proteins is covalently bound to an oligonucleotide. In some embodiments, the oligonucleotide comprises a barcode oligonucleotide. In some embodiments, the oligonucleotide comprises a sequence having at least 60%, at least 70%, at least 80%, at least 90%, or 100% identity to a sequence set forth in any one of SEQ ID NOs: 1-55 as shown in Table 2. In some embodiments, the oligonucleotide comprises a sequence as set forth in any one of SEQ ID NOs: 1-55 as shown in Table 2. In some embodiments, each of the carbohydrate binding proteins are conjugated to an oligonucleotide as shown in Table 3.WSGR Docket No.: 42256-622.601 Table 2. Exemplary Oligonucleotide SequencesWSGR Docket No.: 42256-622.601Table 3. Exemplary Carbohydrate Binding Protein-Oligonucleotide ConjugatesWSGR Docket No.: 42256-622.601WSGR Docket No.: 42256-622.601

[0133] Also provided herein is a composition comprising a sample comprising cells embedded onto a planar surface. In some embodiments, the composition further comprises a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to a different oligonucleotide. In some embodiments, the composition further comprises a corresponding plurality of fluorescently labeled nucleic acid probes, wherein each fluorescently labeled nucleic acid probe is configured to specifically bind to only one of the oligonucleotides. In some embodiments, the sample is labeled with the plurality of carbohydrate binding proteins.

[0134] In some embodiments, the carbohydrate binding protein is a lectin. In some embodiments the carbohydrate binding protein is a mannose-binding protein. In some embodiments, the carbohydrate binding protein is an enzyme. In some embodiments, the carbohydrate binding protein is a catalytically inactivated enzyme. In some embodiments, the catalytically inactivated enzyme is a glycosylase. In some embodiments, the catalytically inactivated enzyme is a transferase. In some embodiments, the catalytically inactivated enzyme is inactivated by one or more mutations. In some embodiments, the catalytically inactivated enzyme is inactivated by truncation.WSGR Docket No.: 42256-622.601

[0135] In some embodiments, the plurality of carbohydrate binding proteins comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, or at least 50 different carbohydrate binding proteins. In some embodiments, the plurality of carbohydrate binding proteins comprises about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, or about 50 different carbohydrate binding proteins. In some embodiments, the plurality of carbohydrate binding proteins comprises a carbohydrate binding protein listed in Table 1 or Table 3 or two or more of the carbohydrate binding proteins listed in Table 1 or Table 3. Kits

[0136] Provided herein is a kit comprising a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to an oligonucleotide. In some embodiments, each carbohydrate binding protein is covalently bound to a different oligonucleotide. In some embodiments, a subset of the plurality of carbohydrate binding proteins is covalently bound to a first oligonucleotide. In some embodiments, an additional subset of the plurality of carbohydrate binding proteins is covalently bound to a second oligonucleotide. In some embodiments, the first oligonucleotide and the second oligonucleotide are same. In some embodiments, the first oligonucleotide and the second oligonucleotide are different. In some embodiments, the kit further comprises a corresponding plurality of fluorescently labeled nucleic acid probes, wherein each nucleic acid probe is configured to specifically bind to only one of the oligonucleotides. In some embodiments, the kit further comprises a denaturing agent capable of removing the nucleic acid probes bound to an oligonucleotide-bound-carbohydrate binding protein. Kits provided herein typically include a label indicating the intended use of the contents of the kit. The term label includes any writing, or recorded material supplied on or with the kit, or which otherwise accompanies the kit. In some embodiments, the plurality of carbohydrate binding proteins comprises a carbohydrate binding protein listed in Table 1 or Table 3, or two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.WSGR Docket No.: 42256-622.601 Methods of Modifying a Carbohydrate Binding Protein

[0137] Provided herein is a method of conjugating a carbohydrate binding protein to an oligonucleotide. In some embodiments, the method comprises contacting a carbohydrate binding protein with dibenzocyclooctyne (DBCO) comprising a tetrafluorophenyl ester group, generating a DBCO-labeled carbohydrate binding protein. In some embodiments, the method further comprises contacting the DBCO-labeled carbohydrate binding protein with an oligonucleotide conjugated to an azide moiety.

[0138] In some embodiments, the oligonucleotide comprises a sequence with at least 60%, at least 70%, at least 80%, at least 90%, or 100% identity to a sequence set forth in any one of SEQ ID NOs: 1-55. In some embodiments, the oligonucleotide comprises a sequence set forth in any one of SEQ ID NOs: 1-55. In some embodiments, the carbohydrate binding protein is selected from the carbohydrate binding proteins listed in Table 1 or Table 3. Computer Implemented Methods for Analyzing a Sample

[0139] Provided herein is a computer implemented method for analyzing a sample. In some embodiments, the method comprises receiving input comprising images of a sample, wherein the images of a sample comprise the images generated by the methods of imaging disclosed herein. In some embodiments, the method further comprises generating, e.g., using a machine learning algorithm, an output comprising a quantitative or qualitative value of functional or structural features of the sample.

[0140] In some embodiments, the sample comprises a whole tissue. In some embodiments, the sample comprises a tissue section. In some embodiments, the tissue is obtained from muscle. In some embodiments, the sample is obtained from skeletal muscle. In some embodiments, the sample is obtained from smooth muscle. In some embodiments, the sample is obtained from cardiac muscle. In some embodiments, the sample is obtained from brain. In some embodiments, the sample is obtained from a nerve. In some embodiments, the tissue is obtained from a sciatic nerve. In some embodiments, the sample is obtained from spinal cord. In some embodiments, the sample is obtained from kidney. In some embodiments, the sample is obtained from liver. In some embodiments, the sample is obtained from lung. In some embodiments, the sample is obtained from lymph node. In some embodiments, the sample is obtained from spleen. In some embodiments, the sample is obtained from intestine. In some embodiments, the sample is obtained from skin. In some embodiments, the sample is obtained from eye. In some embodiments, the sample is obtained from bone. In some embodiments, the sample is obtained from a tumor. In some embodiments, the sample is fixed. In some embodiments, the sample is not fixed.WSGR Docket No.: 42256-622.601 Methods of Detecting a Tissue Pathology

[0141] Also provided herein is a method of detecting a tissue pathology. In some embodiments, the method comprises obtaining a tissue sample. In some embodiments, the method further comprises applying the method of any of the foregoing embodiments to the tissue sample. In some embodiments, the tissue sample comprises cancer cells. In some embodiments, the tissue sample comprises cells comprising a disorder of glycosylation. In some embodiments, the tissue sample comprising cancer cells or cells comprising a disorder of glycosylation comprises a glycosylation pattern that is different from a tissue sample that does not comprise cancer cells or cells comprising a disorder of glycosylation. In some embodiments, the tissue sample comprising cancer cells or cells comprising a disorder of glycosylation comprises a lower or higher expression level of the fluorescently labeled nucleic acid probes of any of the foregoing embodiments. In some embodiments, the disorder of glycosylation comprises Saul-Wilson Syndrome (SWS) or GNE myopathy. In some embodiments, the cancer is pancreatic ductal adenocarcinoma (PDAC). Methods of Characterizing a Cancer

[0142] Also provided herein is a method of characterizing a cancer in a subject. In some embodiments, the method comprises obtaining a tissue sample from the subject. In some embodiments, the tissue sample comprises a cancer tissue. In some embodiments, the method comprises applying the method of any of the foregoing embodiments to the tissue sample. In some embodiments, the cancer is pancreatic ductal adenocarcinoma (PDAC). In some embodiments, characterizing comprises identifying a border between the cancer tissue and healthy tissue in the tissue sample. In some embodiments, the border is identified by detecting a lower or higher expression level of the fluorescently labeled nucleic acid probes of any one of the preceding embodiments by the cancer tissue compared to the healthy tissue. In some embodiments, characterizing comprise determining the size of the tumor. In some embodiments, characterizing comprises determining progression of the tumor. In some embodiments, progression is measured by comparing the results obtained from a first tissue sample to the results obtained from a second tissue sample. In some embodiments, the second tissue sample is obtained at least one day, at least one week, at least 2 weeks, at least one month, at least 3 months, at least 6 months, at least one year, at least two years, at least five years later than the first tissue sample. Diseases and Tissues

[0143] The methods and compositions disclosed herein may be used in the diagnosis or monitoring of a disease affecting a tissue. In some embodiments, the is a disease characterized by tissue specific increased or decreased expression of a carbohydrate. In some embodiments,WSGR Docket No.: 42256-622.601 the disease is cancer. In some embodiments, the cancer is selected from the group consisting of carcinoma, lymphoma, blastoma, sarcoma, leukemia, squamous cell cancer, lung cancer (including small cell lung cancer, non-small cell lung cancer (NSCLC), adenocarcinoma of the lung, and squamous carcinoma of the lung), cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer (including gastrointestinal cancer), pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, melanoma, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, head and neck cancer, colorectal cancer, rectal cancer, soft-tissue sarcoma, Kaposi’s sarcoma, B-cell lymphoma, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), myeloma, Hairy cell leukemia, chronic myeloblasts leukemia, and post-transplant lymphoproliferative disorder (PTLD), and combinations thereof.

[0144] In some embodiments, the disease is aging. In some embodiments the disease is a degenerative disease. In some embodiments, the disease is muscular dystrophy. In some embodiments, the tissue is muscle. In some embodiments, the tissue is skeletal muscle. In some embodiments, the tissue is smooth muscle. In some embodiments, the tissue is cardiac muscle. In some embodiments, the tissue is brain. In some embodiments, the tissue is a nerve. In some embodiments, the tissue is a sciatic nerve. In some embodiments, the tissue is spinal cord. In some embodiments, the tissue is kidney. In some embodiments, the tissue is liver. In some embodiments, the tissue is lung. In some embodiments, the tissue is lymph node. In some embodiments, the tissue is spleen. In some embodiments, the tissue is intestine. In some embodiments, the tissue is skin. In some embodiments, the tissue is eye. In some embodiments, the tissue is bone. In some embodiments, the tissue is cartilage. In some embodiments, the tissue is a tumor. EXAMPLES

[0145] The following examples are provided to further illustrate some embodiments of the present disclosure but are not intended to limit the scope of the disclosure; it will be understood by their exemplary nature that other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used. Example 1. Generation of Oligonucleotide-conjugated Carbohydrate binding proteins

[0146] Oligonucleotides were conjugated onto either carbohydrate binding proteins or antibodies via a click chemistry reaction in order to assess the efficiency of conjugation. First, the protein was concentrated. A 50 kDa Molecular Weight Cutoff (MWCO) filter, for IgG antibodies, or 10 kDa MWCO filter for lectins was blocked with 400 µL of 0.05% Tween inWSGR Docket No.: 42256-622.601 PBS and centrifuged at 12000xg for 8 mins. Protein content was measured from a master tube via Nanodrop by measuring absorbance at 280 nm. Then, 50 µg of protein (either glycan- binding proteins or IgG antibodies) was added to the column with 400 µL of PBS to wash. The column was centrifuged at 12000xg for 8 mins and the flow through was discarded. The protein was resuspended in 100 µL of PBS.

[0147] To add dibenzocylooctyne (DBCO) groups for the click chemistry reaction, 0.25 µL (12.5 nmols) of 50 mM Sulfo DBCO-PEG4-TFP was added to the column and allowed to react for 4 hrs at room temperature. The column was washed with 400 µL of PBS and centrifuged at 12000xg for 8 mins. To confirm conjugation efficiency, 100 µL of PBS was added and protein absorbance was measured using a Nanodrop spectrophotometer. Peaks were measured at 309 nm (DBCO), 280 nm (antibody or carbohydrate binding protein), 260 nm and 230 nm (Ethanol and DNA contaminants). The rate of DBCO addition was calculated to confirm that between 3 and 10 DBCO molecules were added to each protein molecule. The optimal level of conjugation for both antibodies and carbohydrate binding proteins was estimated by establishing the dynamic range of fluorescence after conjugation with increasing amounts of DBCO, as shown in FIGs. 1A-1C and FIG.2.400 µL of PBS was added to the column and centrifuged at 12000xg for 8 min.

[0148] To conjugate DNA oligonucleotide barcodes to the antibodies or carbohydrate binding proteins, 50 µL of the azide-modified oligonucleotide (250 nmols) was added to the column and allowed to react overnight at room temperature.400 µL of Tris-EDTA (TE, 10 mM Tris and 1 mM EDTA) buffer was added and centrifuged at 12000xg for 8 min.400 µL of high salt PBS (1 M NaCl in PBS) was added, and the samples were vortexed, at centrifuged at 12000xg for 8mins. Samples were collected in 200 µL per 50 µg of antibody or carbohydrate binding protein of a protein stabilization solution (1:1000.5 M EDTA and 1:1001% sodium azide) and stored at 4 ºC. Example 2. Tissue Staining with Oligonucleotide-Conjugated Carbohydrate Binding Proteins

[0149] The oligonucleotide-conjugated carbohydrate binding proteins generated as in Example 1 were used in imaging samples to assess the capability of the carbohydrate binding proteins to identify a glycan profile in the sample. The panel comprised 11 different oligonucleotide- conjugated carbohydrate binding proteins. Muscle tissue was obtained from mice and fixed. Thin sections of skeletal muscle were affixed onto 0.1% gelatin-coated #1 glass slides. Staining reagents were prepared by mixing oligonucleotide-conjugated antibodies or carbohydrate binding proteins. As negative controls, non-fluorescent complementary DNA oligonucleotides of each barcode at 500 µM, a combination of IgG molecules from mouse, rat and rabbit at 10WSGR Docket No.: 42256-622.601 µg / mL, and salmon sperm DNA were also prepared. The tissue slides were incubated with the staining reagents for 3 hr at room temperature or overnight at 4 ºC. Following incubation, samples were washed with PBS and fixed with 1.6% paraformaldehyde, then methanol, and then bis(sulfosuccinimidyl)suberate (BS3).

[0150] Tissue slides were then imaged using an iterative rendering process by serially applying a subset of fluorescently tagged oligonucleotides complementary to a subset of the oligonucleotides bound to the carbohydrate binding proteins or antibodies, capturing an image, denaturing the oligonucleotide binding, washing away the subset of fluorescently tagged oligonucleotides complementary with DMSO, applying a new subset of fluorescently tagged oligonucleotides, and repeating this process until all carbohydrate binding proteins or antibodies have been captured. This process is illustrated in FIG.9 and FIG.10A. Images obtained using carbohydrate binding proteins (FIG.3A), demonstrated staining patterns illustrating glycan expression profiles in the skeletal muscle tissue. Images obtained using antibodies (FIG.3B) identified specific cell types in the tissue.

[0151] Additionally, carbohydrate binding protein binding profiles were obtained in various subcellular locations including the nucleus, the perinuclear region, the cytoplasm, the cell membrane, and the extracellular matrix (FIGs.4A-4E). FIG.4A depicts nuclear staining; FIG. 4B depicts peri-nuclear staining; FIG.4C depicts cytoplasmic staining; FIG.4D depicts cell membrane staining; and FIG.4E depicts extracellular matrix (ECM) staining.

[0152] Other tissue samples were also used, including samples taken from neuromuscular junctions and muscle spindles (FIGs.5A and 5B). FIG.5A depicts muscle fiber (LCA) and NMJ (VVL) staining. FIG.5B depicts staining of vessels (DSL), muscle spindles (PHAE), and motor nerves (ECL). Example 3. AI-Powered Method of Tissue Analysis

[0153] Images generated from highly multiplexed glycan imaging were used to train an AI model to classify different structures within tissue sections using combinations of biomarkers (carbohydrate binding proteins and antibodies) (FIG.6). Antibodies against cell surface markers, cytoplasmic proteins, or nuclear transcription factors were used to localize specific cell types within the tissue. Segmentation masks that demarcate the shape of each cell and / or its nuclei were dilated or eroded to create areas that represent the entire cell (full cell mask), the cell membrane (full – an eroded cell mask), the cytoplasm (eroded cell mask – nuclei mask), perinuclear regions (dilated nuclei mask), and the cell nuclei (nuclei mask), or any combinations thereof. The intensity of staining within each mask region was used to quantify the staining of glycan-binding protein, and thereby the presence and composition of glycan moieties in each cellular compartment. Moreover, morphological features of each cell including cell area, shape,WSGR Docket No.: 42256-622.601 and position was extracted and quantified. This was used to quantify metrics including capillary counts, myofiber counts, and myofiber sizes (FIGs.7A-7C). FIG.7A depicts the capillary count; FIG.7B depicts the myofiber count; FIG.7C depicts the myofiber size. The AI model was trained to distinguish healthy (FIG.8A) from denervated (FIG.8B) or regenerating (FIG. 8C) cells. Example 4. Application of AI-Powered Method of Tissue Analysis

[0154] Quantified glycan-binding staining can be calculated based on cell type and its localization within the tissue, or the presence of nearby cell types or tissue features. Moreover, comparisons of cell type or tissue structures can be made to identify changes glycosylation across disease states (healthy vs. injured, aging, or degenerating) or correlated to tissue function (i.e. contraction strength of skeletal muscle, insulin secretion of pancreas, aggressiveness of tumor growth) or in response to a drug treatment (e.g., tumor cells in response to a chemotherapy, the location of CAR-T cells within a tumor, restoration of the Dystroglycan complex by a gene therapy). An exemplary workflow of this analysis is shown in FIG.10B. Example 5. Glycosylation Patterns of Abnormal Human Skeletal Development

[0155] To identify glycosylation patterns in abnormal skeletal development related to Saul- Wilson Syndrome (SWS) osteo-chondral organoids were generated either from healthy human induced pluripotent stem cells (iPSCs) or from iPSCs bearing a mutated COG4, which causes SWS. SWS is a congenital disorder of glycosylation characterized by short stature (dwarfism) and skeletal abnormalities. Control and SWS organoids were cultured for 21 days, and the glycosylation patterns of the organoids were assayed using the methods detailed in Examples 1 and 2. During chondrogenic differentiation, glycosylation analysis captured significant changes in glycosylation profiles across organoid structures between days 14 and 21 of culture. As shown in FIG.11, at the earlier timepoint, cells in the outer layer of the organoid were heavily glycosylated with Galactose moieties, whereas cells in the inner layer are weakly positive for GalNAc and Lactose. By day 21, the organoid developed a more complex morphology with multiple layers, each exhibiting enrichment in distinct glycan moieties compared to day 14. In contrast, organoids derived from iPSCs carrying SWS patient mutations in COG4 displayed an immature morphology and an abnormal glycan profile and resembled control organoids at day 14, suggesting delayed or stalled development. Thus, this method can provide insight on human developmental processes and defects associated with aberrant glycosylation dynamics in known glycosylation disorders.WSGR Docket No.: 42256-622.601 Example 6. Differential Glycosylation Patterns Delineate Healthy and Tumor Pancreatic Tissues

[0156] To determine whether tissue staining with oligonucleotide-conjugated carbohydrate binding proteins via a method as disclosed herein can reveal tumor-specific glycosylation patterns, tissue samples were obtained from a mouse model of pancreatic ductal adenocarcinoma (PDAC). PDAC is a highly aggressive cancer with a poor prognosis, often presenting undetectable early symptoms. Therefore, PDAC can be challenging to diagnose at an early stage when treatment would be most effective. Current methods used clinically to examine tissue samples and identify clinical histological patterns can be time-consuming depending on the markers used to detect tumors.

[0157] The glycosylation patterns of the samples were assayed using the methods detailed in Examples 1 and 2. As shown in FIG.12, the tumor tissue regions of the tissue sample demonstrated a distinct glycosylation pattern compared to healthy tissue. Notably, healthy tissue is enriched for sialic acid expression compared to the tumor tissue. Identification of these differences can lead to rapid determination of tumor size and boundaries, opening avenues to earlier detection and treatment. Moreover, these findings demonstrate the potential for glycan- based biomarkers in cancer diagnosis. Example 7. Glycosylation Patterns in Muscle Biopsies of Patients with GNE Myopathy

[0158] To determine whether the method can detect differential glycosylation patterns associated with GNE myopathy, muscle biopsies were obtained from patients with GNE myopathy and healthy controls. GNE myopathy is a rare genetic muscle disorder caused by mutations in the GNE gene, which encodes an essential enzyme responsible for sialic acid biosynthesis and regulates cell surface sialylation, a type of glycosylation. Samples were analyzed using the methods detailed in Examples 1 and 2. Analysis of the glycosylation patterns of the human muscle biopsies revealed changes in lectin-binding patterns of GNE patients compared to healthy controls (FIG.13). The analysis detected changes of β-3GalNAc moieties in the muscle fibers as well as glycosylation-related changes corresponding to fibrosis with the accumulation of Mannose moieties in the extracellular matrix. Taken together, these results highlight important regional pathology within a heterogeneously degenerating tissue that can only be revealed by combinations of glycan moieties.

[0159] While preferred embodiments of the present disclosure have been shown and described herein, it will be apparent to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicingWSGR Docket No.: 42256-622.601 the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

WSGR Docket No.: 42256-622.601 CLAIMS What is claimed is:

1. A method of imaging a sample, the method comprising: i) contacting the sample with (a) a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to an oligonucleotide; and (b) a subset of a plurality of fluorescently labeled nucleic acid probes, wherein each nucleic acid probe specifically binds to only one of the oligonucleotides of (i)(a), thereby generating a probe / carbohydrate binding protein complex; ii) imaging the sample to detect a binding of each of the probe / carbohydrate binding protein complexes of step (i)(b); and iii) removing the probes bound to the carbohydrate binding proteins in step (i)(b), wherein the carbohydrate binding proteins remain bound to the sample.

2. The method of claim 1, further comprising repeating steps (i) to (iii) with a different subset of the plurality of fluorescently labeled nucleic acid probes of (i)(b) until all subsets of the plurality of fluorescently labeled nucleic acid probes have been utilized.

3. The method of claim 1 or 2, wherein the plurality of carbohydrate binding proteins comprises a lectin.

4. The method of any one of claims 1-3, wherein the plurality of carbohydrate binding proteins comprises a mannose-binding protein.

5. The method of any one of claims 1-4, wherein the plurality of carbohydrate binding proteins comprises a catalytically inactivated enzyme.

6. The method of claim 5, wherein the catalytically inactive enzyme is a glycosylase.

7. The method of claim 5, wherein the catalytically inactive enzyme is a transferase.

8. The method of any one of claims 5-7, wherein the catalytically inactive enzyme is inactivated by one or more mutations.

9. The method of any one of claims 5-8, wherein the catalytically inactive enzyme is inactivated by truncation.

10. The method of any one of claims 1-9, wherein the plurality of carbohydrate binding proteins comprises about 5, about 10, about 15, about 20, about 25, about 30, about 35, or about 40 different carbohydrate binding proteins.

11. The method of any one of claims 1-10, wherein the plurality of carbohydrate binding proteins comprises two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.WSGR Docket No.: 42256-622.601 12. The method of any one of claims 1-11, wherein plurality of carbohydrate binding proteins comprises a recombinant protein.

13. The method of any one of claims 1-12, wherein the carbohydrate binding protein is covalently bound to the oligonucleotide via a copper-free click chemistry reaction.

14. The method of any one of claims 1-13, wherein each carbohydrate binding protein of the plurality of carbohydrate binding proteins is covalently bound to from 1 to about 15 copies of the oligonucleotide.

15. The method of any one of claims 1-14, wherein the sample comprises a whole tissue.

16. The method of any one of claims 1-14, wherein the sample comprises a tissue section.

17. The method of claim 15 or 16, wherein the sample is obtained from muscle, brain, a nerve, a sciatic nerve, spinal cord, kidney, liver, heart, lung, lymph node, spleen, or intestine tissue.

18. The method of any one of claims 1-17, wherein the sample is fixed.

19. The method of any one of claims 1-17, wherein the sample is not fixed.

20. The method of any one of claims 1-19, wherein step (iii) comprises contacting the sample with DMSO or formamide.

21. The method of any one of claims 1-20, wherein the plurality of carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 9;WSGR Docket No.: 42256-622.601 ix) RCA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 31;WSGR Docket No.: 42256-622.601 xxvi) ACA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 49;WSGR Docket No.: 42256-622.601 xliii) GSL2 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO:

55.

22. The method of any one of claims 1-20, wherein the plurality of carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having a sequence of SEQ ID NO: 20;WSGR Docket No.: 42256-622.601 xviii) UEA II bound to an oligonucleotide having a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having a sequence of SEQ ID NO: 53;WSGR Docket No.: 42256-622.601 xlvii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having a sequence of SEQ ID NO:

55.

23. A method of imaging a sample, the method comprising: i) contacting the sample with a plurality of different carbohydrate binding proteins, wherein each different carbohydrate binding protein of the plurality of different carbohydrate binding proteins is covalently bound to a barcode oligonucleotide of a plurality of barcode oligonucleotides, wherein, upon the contacting, a subset of the plurality of different carbohydrate binding proteins binds to the sample; ii) contacting the sample with a plurality of fluorescently labeled first nucleic acid probes, wherein each fluorescently labeled first nucleic acid probe of the plurality of fluorescently labeled first nucleic acid probes binds to a first barcode oligonucleotide of the plurality of barcode oligonucleotides of step (i), thereby generating a first binary complex of the fluorescently labeled first nucleic acid probe / first barcode oligonucleotide; iii) imaging the sample to detect a presence or absence of the first binary complex of step (ii); and iv) removing the plurality of fluorescently labeled first nucleic acid probes from the sample, wherein the subset of the plurality of different carbohydrate binding proteins remain bound to the sample.

24. The method of claim 23, further comprising: (ii’) contacting the sample with a plurality of fluorescently labeled second nucleic acid probes, wherein each fluorescently labeled second nucleic acid probe of the plurality of fluorescently labeled second nucleic acid probes is configured to bind to a second barcode oligonucleotide of the plurality of barcode oligonucleotides of step (i), thereby generating a second binary complex of the fluorescently labeled second nucleic acid probe / second barcode oligonucleotide; (iii’) imaging the sample to detect a presence or absence of the second binary complex of step (ii’); and (iv’) removing the plurality of fluorescently labeled second nucleic acid probes from the sample, wherein the subset of the plurality of different carbohydrate binding proteins remain bound to the sample.

25. The method of claim 23 or 24, further comprising: repeating steps (ii) to (iv) multiple times, each time with a plurality of fluorescently labeled additional nucleic acid probes, wherein each fluorescently labeled additional nucleic acid probe of the plurality ofWSGR Docket No.: 42256-622.601 fluorescently labeled additional nucleic acid probes is configured to bind to an additional barcode oligonucleotide of the plurality of barcode oligonucleotides of step (i).

26. The method of any one of claims 23-25, wherein the imaging comprises measuring a staining intensity.

27. The method of any one of claims 23-26, wherein the plurality of different carbohydrate binding proteins comprises one or more lectins.

28. The method of any one of claims 23-27, wherein the plurality of different carbohydrate binding proteins comprises one or more mannose-binding proteins.

29. The method of any one of claims 23-28, wherein the plurality of different carbohydrate binding protein comprises one or more catalytically inactivated enzymes.

30. The method of claim 29, wherein the one or more catalytically inactive enzymes comprise a glycosylase.

31. The method of claim 29, wherein the one or more catalytically inactive enzymes comprise a transferase.

32. The method of any one of claims 29-31, wherein the one or more catalytically inactive enzymes comprise an enzyme inactivated by one or more mutations.

33. The method of any one of claims 29-31, wherein the one or more catalytically inactive enzymes comprise an enzyme inactivated by truncation.

34. The method of any one of claims 23-33, wherein the plurality of different carbohydrate binding proteins comprises about 5, about 10, about 15, about 20, about 25, about 30, about 35, or about 40 different carbohydrate binding proteins.

35. The method of any one of claims 23-34, wherein the plurality of different carbohydrate binding proteins comprises two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.

36. The method of any one of claims 23-35, wherein the plurality of different carbohydrate binding protein comprises a recombinant protein.

37. The method of any one of claims 23-36, wherein each carbohydrate binding protein of the plurality of different carbohydrate binding proteins is covalently bound to the barcode oligonucleotide via a copper-free click chemistry reaction.

38. The method of any one of claims 23-37, wherein each different carbohydrate binding protein of the plurality of different carbohydrate binding proteins is covalently bound to from 1 to about 15 copies of the barcode oligonucleotide.

39. The method of any one of claims 23-38, wherein the sample comprises a whole tissue.

40. The method of any one of claims 23-38, wherein the sample comprises a tissue section.WSGR Docket No.: 42256-622.601 41. The method of claim 39 or 40, wherein the sample is obtained from muscle, brain, a nerve, a sciatic nerve, spinal cord, kidney, liver, heart, lung, lymph node, spleen, or intestine tissue.

42. The method of any one of claims 23-41, wherein the sample is fixed.

43. The method of any one of claims 23-41, wherein the sample is not fixed.

44. The method of any one of claims 23-43, wherein step (iv) comprises contacting the sample with DMSO or formamide.

45. The method of any one of claims 23-44, wherein the plurality of different carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 15;WSGR Docket No.: 42256-622.601 xiii) HPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 35;WSGR Docket No.: 42256-622.601 xxx) GS II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 53;WSGR Docket No.: 42256-622.601 xlvii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO:

55.

46. The method of any one of claims 23-44, wherein the plurality of different carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having a sequence of SEQ ID NO: 27;WSGR Docket No.: 42256-622.601 xxiii) SNA II bound to an oligonucleotide having a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having a sequence of SEQ ID NO:

55.

47. A composition comprising a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to an oligonucleotide, and wherein the oligonucleotide comprises a sequence having at least 80% identity to a sequence set forth in any one of SEQ ID NOs: 1-55.WSGR Docket No.: 42256-622.601 48. The composition of claim 47, wherein the oligonucleotide comprises a sequence set forth in any one of SEQ ID NOs: 1-55.

49. A composition comprising: i) a sample comprising cells embedded onto a planar surface; ii) a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to a different oligonucleotide; and iii) a plurality of fluorescently labeled nucleic acid probes, wherein each nucleic acid probe specially binds to only one of the oligonucleotides.

50. The composition of any one of claims 47-49, wherein the plurality of carbohydrate binding proteins comprise a lectin.

51. The composition of any one of claims 47-50, wherein the plurality of carbohydrate binding proteins comprises a mannose-binding protein.

52. The composition of any one of claims 47-51, wherein the plurality of carbohydrate binding proteins comprises a catalytically inactivated enzyme.

53. The composition of claim 52, wherein the catalytically inactive enzyme is a glycosylase.

54. The composition of claim 52, wherein the catalytically inactive enzyme is a transferase.

55. The composition of any one of claims 52-54, wherein the catalytically inactive enzyme is inactivated by one or more mutations.

56. The composition of any one of claims 52-54, wherein the catalytically inactive enzyme is inactivated by truncation.

57. The composition of any one of claims 47-56, wherein the plurality of carbohydrate binding proteins comprises a carbohydrate binding protein listed in Table 1 or Table 3, or two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.

58. The composition of any one of claims 47-57, wherein the plurality of carbohydrate binding proteins comprises two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 5;WSGR Docket No.: 42256-622.601 v) TL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 24;WSGR Docket No.: 42256-622.601 xxii) LOTUS bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 45;WSGR Docket No.: 42256-622.601 xxxix) MPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO:

55.

59. The composition of any one of claims 47-57, wherein the plurality of carbohydrate binding proteins comprises two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide of SEQ ID NO: 5; v) TL bound to an oligonucleotide of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide of SEQ ID NO: 10; x) SBA bound to an oligonucleotide of SEQ ID NO: 11; xi) CA bound to an oligonucleotide of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide of SEQ ID NO: 15;WSGR Docket No.: 42256-622.601 xiii) HPA bound to an oligonucleotide of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide of SEQ ID NO: 54; andWSGR Docket No.: 42256-622.601 xlviii) PHAE bound to an oligonucleotide of SEQ ID NO:

55.

60. A kit comprising: i) a plurality of carbohydrate binding proteins, wherein each carbohydrate binding protein is covalently bound to a different oligonucleotide; ii) a plurality of fluorescently labeled nucleic acid probes, wherein each nucleic acid probe is configured to specifically bind to only one of the oligonucleotides of step (i); and iii) a denaturing agent capable of removing a nucleic acid probe that is bound to an oligonucleotide-bound-carbohydrate binding protein.

61. The kit of claim 60, wherein the plurality of carbohydrate binding proteins comprises a carbohydrate binding protein listed in Table 1 or Table 3, or two or more of the carbohydrate binding proteins listed in Table 1 or Table 3.

62. The kit of claim 60 or 61, wherein the plurality of carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 11;WSGR Docket No.: 42256-622.601 xi) CA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 22; xx) Jacalin AIA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 33;WSGR Docket No.: 42256-622.601 xxviii) VVL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 51;WSGR Docket No.: 42256-622.601 xlv) DSL bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having at least 80% sequence identity to a sequence of SEQ ID NO:

55.

63. The kit of claim 60 or 61, wherein the plurality of carbohydrate binding proteins comprise two or more oligonucleotide-bound carbohydrate binding proteins selected from the group consisting of: i) HHA bound to an oligonucleotide having a sequence of SEQ ID NO: 1; ii) CSA bound to an oligonucleotide having a sequence of SEQ ID NO: 2; iii) TKA bound to an oligonucleotide having a sequence of SEQ ID NO: 3; iv) MNAG bound to an oligonucleotide having a sequence of SEQ ID NO: 5; v) TL bound to an oligonucleotide having a sequence of SEQ ID NO: 6; vi) WFA bound to an oligonucleotide having a sequence of SEQ ID NO: 7; vii) ECA bound to an oligonucleotide having a sequence of SEQ ID NO: 8; viii) LEA bound to an oligonucleotide having a sequence of SEQ ID NO: 9; ix) RCA I bound to an oligonucleotide having a sequence of SEQ ID NO: 10; x) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 11; xi) CA bound to an oligonucleotide having a sequence of SEQ ID NO: 13; xii) PTA Galactose bound to an oligonucleotide having a sequence of SEQ ID NO: 15; xiii) HPA bound to an oligonucleotide having a sequence of SEQ ID NO: 16; xiv) PTA GalNAc bound to an oligonucleotide having a sequence of SEQ ID NO: 17; xv) MNAM bound to an oligonucleotide having a sequence of SEQ ID NO: 18; xvi) SNA I bound to an oligonucleotide having a sequence of SEQ ID NO: 19; xvii) WGA bound to an oligonucleotide having a sequence of SEQ ID NO: 20; xviii) UEA II bound to an oligonucleotide having a sequence of SEQ ID NO: 21; xix) ASA bound to an oligonucleotide having a sequence of SEQ ID NO: 22;WSGR Docket No.: 42256-622.601 xx) Jacalin AIA bound to an oligonucleotide having a sequence of SEQ ID NO: 23; xxi) NPA bound to an oligonucleotide having a sequence of SEQ ID NO: 24; xxii) LOTUS bound to an oligonucleotide having a sequence of SEQ ID NO: 27; xxiii) SNA II bound to an oligonucleotide having a sequence of SEQ ID NO: 28; xxiv) UDA bound to an oligonucleotide having a sequence of SEQ ID NO: 29; xxv) STA bound to an oligonucleotide having a sequence of SEQ ID NO: 31; xxvi) ACA bound to an oligonucleotide having a sequence of SEQ ID NO: 32; xxvii) CONA bound to an oligonucleotide having a sequence of SEQ ID NO: 33; xxviii) VVL bound to an oligonucleotide having a sequence of SEQ ID NO: 34; xxix) GNA bound to an oligonucleotide having a sequence of SEQ ID NO: 35; xxx) GS II bound to an oligonucleotide having a sequence of SEQ ID NO: 36; xxxi) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 37; xxxii) Jacalin bound to an oligonucleotide having a sequence of SEQ ID NO: 38; xxxiii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 40; xxxiv) PHAL bound to an oligonucleotide having a sequence of SEQ ID NO: 41; xxxv) MAA bound to an oligonucleotide having a sequence of SEQ ID NO: 42; xxxvi) DBA bound to an oligonucleotide having a sequence of SEQ ID NO: 43; xxxvii) STL bound to an oligonucleotide having a sequence of SEQ ID NO: 44; xxxviii) ECL bound to an oligonucleotide having a sequence of SEQ ID NO: 45; xxxix) MPA bound to an oligonucleotide having a sequence of SEQ ID NO: 46; xl) SBA bound to an oligonucleotide having a sequence of SEQ ID NO: 47; xli) UEA I bound to an oligonucleotide having a sequence of SEQ ID NO: 48; xlii) LEL bound to an oligonucleotide having a sequence of SEQ ID NO: 49; xliii) GSL2 bound to an oligonucleotide having a sequence of SEQ ID NO: 50; xliv) GSL1 bound to an oligonucleotide having a sequence of SEQ ID NO: 51; xlv) DSL bound to an oligonucleotide having a sequence of SEQ ID NO: 52; xlvi) LCA bound to an oligonucleotide having a sequence of SEQ ID NO: 53; xlvii) PSA bound to an oligonucleotide having a sequence of SEQ ID NO: 54; and xlviii) PHAE bound to an oligonucleotide having a sequence of SEQ ID NO: 55.WSGR Docket No.: 42256-622.601 64. A method of conjugating a carbohydrate binding protein to an oligonucleotide, the method comprising: i) contacting the carbohydrate binding protein with dibenzocyclooctyne (DBCO) comprising a tetrafluorophenyl ester group, thereby generating a DBCO-labeled carbohydrate binding protein; and ii) contacting the DBCO-labeled carbohydrate binding protein with an oligonucleotide, wherein the oligonucleotide is conjugated to an azide moiety; thereby conjugating the carbohydrate binding protein to the oligonucleotide.

65. The method of claim 64, wherein the oligonucleotide comprises sequence having at least 80% identity to a sequence set forth in any one of SEQ ID NOs: 1-55.

66. The method of claim 64, wherein the oligonucleotide comprises sequence set forth in any one of SEQ ID NOs: 1-55.

67. The method of any one of claims 64-66, wherein the carbohydrate binding protein is selected from the carbohydrate binding proteins listed in Table 1 or Table 3.

68. A computer implemented method for analyzing a sample, the method comprising: i) receiving input comprising images of the sample, wherein the images of the sample comprise images generated by the method of any one of claims 1-46; and ii) generating, using a machine learning algorithm, an output comprising a quantitative or qualitative value of functional or structural features of the sample.

69. A method of detecting a tissue pathology, the method comprising: i) obtaining a tissue sample; and ii) applying the method of any one of claims 1-46 to the tissue sample.

70. The method of claim 69, wherein the tissue sample comprises cancer cells.

71. The method of claim 69 or 70, wherein the tissue sample comprises cells comprising a disorder of glycosylation.

72. The method of claim 70 or 71, wherein the tissue sample comprises a glycosylation pattern that is different from a tissue sample that does not comprise cancer cells or cells comprising a disorder of glycosylation.

73. The method of claim 72, wherein the tissue sample comprises a lower or higher expression level of the fluorescently labeled nucleic acid probes of any one of claims 1- 46.

74. The method of any one of claims 71-73, wherein the disorder of glycosylation comprises Saul-Wilson Syndrome (SWS) or GNE myopathy.

75. The method of any one of claims 70-73, wherein the cancer is pancreatic ductal adenocarcinoma (PDAC).WSGR Docket No.: 42256-622.601 76. A method of characterizing a cancer in a subject, the method comprising: i) obtaining a tissue sample from the subject, wherein the tissue sample comprises a cancer tissue; and ii) applying the method of any one of claims 1-46 to the tissue sample.

77. The method of claim 76, wherein the cancer is pancreatic ductal adenocarcinoma (PDAC).

78. The method of claim 76 or 77, wherein the characterizing comprises identifying a border between the cancer tissue and a healthy tissue in the tissue sample.

79. The method of claim 78, wherein the border is identified by detecting a lower or higher expression level of the fluorescently labeled nucleic acid probes of any one of claims 1- 46 by the cancer tissue compared to the healthy tissue.

80. The method of any one of claims 78 or 79, wherein the characterizing comprises determining a size of a tumor.

81. The method of claim 80, wherein the characterizing comprises determining progression of the tumor.

82. The method of claim 81, wherein the progression is measured by comparing results obtained from a first tissue sample to results obtained from a second tissue sample, wherein the second tissue sample is obtained at least one week later than the first tissue sample.

Images