Multiplex capture of gene and protein expression from a biological sample
Provided herein are methods, compositions, and kits for preparing biological samples for multiplex spatial gene expression and proteomic analysis, such as determining a location of a nucleic acid analyte and a protein analyte in a biological sample.
1. A composition comprising:
a) a spatial array comprising a substrate comprising:
(i) a first plurality of capture probes wherein the first plurality of capture probes comprise a spatial barcode and a first plurality of capture domains; and
(ii) a second plurality of capture probes wherein the second plurality of capture probes comprise a spatial barcode and a second plurality of capture domains hybridized to a plurality of oligonucleotides from an analyte capture agent, wherein the analyte capture agent comprises an analyte-binding moiety comprising an antibody or an antigen-binding fragment thereof, and wherein the oligonucleotides comprise an analyte capture sequence and an analyte binding moiety barcode; and
b) a pair of probes comprising:
(i) a plurality of first probes, wherein a first probe of the plurality of first probes is hybridized to a target nucleic acid and
(ii) a plurality of second probes, wherein a second probe of the plurality of second probes is hybridized to the target nucleic acid at a separate location from the first probe and wherein the second probe has a sequence complementary to the first plurality of capture domains.
2. The composition of claim 1 , wherein the first plurality of capture probes further comprise one or more functional domains, a cleavage domain, a unique molecular identifier, and combinations thereof.
3. The composition of claim 1 , wherein the second plurality of capture probes further comprise one or more functional domains, a cleavage domain, a unique molecular identifier, and combinations thereof.
4. The composition of claim 1 , wherein the first plurality of capture domains comprise homopolymeric sequences and the second plurality of capture domains comprise homopolymeric sequences.
5. The composition of claim 1 , wherein the first plurality of capture domains are homopolymeric sequences and the second plurality of capture domains are non-homopolymeric sequences.
6. The composition of claim 1 , wherein the first plurality of capture domains are non-homopolymeric sequences and the second plurality of capture domains are non-homopolymeric sequences.
7. The composition of claim 4 , wherein the first plurality of capture domains and the second plurality of capture domains are poly(T) sequences.
8. The composition of claim 6 , wherein the non-homopolymeric sequences of the first plurality of capture domains and the non-homopolymeric sequences of the second plurality of capture domains are different.
9. The composition of claim 5 , wherein the homopolymeric sequences of the first plurality of capture domains are poly(T) sequences and the non-homopolymeric sequences of the second plurality of capture domains comprise a fixed sequence.
10. The composition of claim 9 , wherein the fixed sequence comprises at least one sequence selected from SEQ ID NO: 1 through SEQ ID NO: 11.
11. The composition of claim 1 , wherein the spatial array further comprises one or more protein dilution series.
12. The composition of claim 1 , wherein the spatial array comprising the substrate comprises a plurality of features, wherein a feature of the plurality of features comprises a bead or a well.
13. The composition of claim 12 , wherein the first plurality of capture probes and the second plurality of capture probes are directly attached to the substrate.
14. The composition of claim 12 , wherein the first plurality of capture probes and the second plurality of capture probes are indirectly attached to the substrate.
15. The composition of claim 1 , wherein the target nucleic acid is DNA.
16. The composition of claim 1 , wherein the target nucleic acid is RNA.
17. The composition of claim 1 , further comprising a RNase.
18. The composition of claim 1 , further comprising a permeabilization reagent.
19. The composition of claim 18 , wherein the permeabilization reagent comprises a protease and a detergent.