Method for transposase-mediated spatial tagging and analyzing genomic DNA in a biological sample
The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.
1. A method for spatial identification of a cell or cell nucleus in a tissue section, the method comprising:
(a) contacting the tissue section with an array comprising a plurality of spatial capture probes, wherein a spatial capture probe of the plurality of spatial capture probes comprises:
(i) a spatial barcode, wherein the spatial barcode identifies a location of the spatial capture probe on the array; and
(ii) a sequence complementary to a capture domain of a cellular capture probe;
(b) incorporating the spatial capture probe into the cell or cell nucleus of the tissue section, wherein the spatial capture probe is proximal to the cell or cell nucleus relative to other cells or cell nuclei in the tissue section, thereby generating a spatially-barcoded cell or cell nucleus; and
(c) dissociating the tissue section into a plurality of partitions, wherein a partition of the plurality of partitions comprises:
(i) the spatially-barcoded cell or cell nucleus; and
(ii) the cellular capture probe, wherein the cellular capture probe comprises:
(1) a cellular barcode, wherein the cellular barcode identifies the partition among the plurality of partitions; and
(2) the capture domain,
wherein (i) a sequence of the spatial barcode or a complement thereof and (ii) a sequence of the cellular barcode or a complement thereof provide spatial identification of the cell or cell nucleus in the tissue section.
2. The method of claim 1 , further comprising hybridizing the sequence complementary to the capture domain of the spatial capture probe to the capture domain of the cellular capture probe.
3. The method of claim 2 , further comprising extending the cellular capture probe using the spatial capture probe as a template.
4. The method of claim 3 , further comprising extending the spatial capture probe using the cellular capture probe as a template.
5. The method of claim 1 , further comprising determining: (i) the sequence of the spatial barcode or the complement thereof and (ii) the sequence of the cellular barcode or the complement thereof.
6. The method of claim 5 , wherein the determining comprises sequencing.
7. The method of claim 1 , wherein the spatial capture probe is coupled to a bead.
8. The method of claim 1 , wherein the cellular capture probe is coupled to a bead.
9. The method of claim 8 , wherein the bead further comprises an additional capture probe, wherein the additional capture probe comprises: (1) a sequence of the cellular barcode; and (2) a poly(T) capture domain.
10. The method of claim 9 , further comprising hybridizing a nucleic acid analyte from the cell or cell nucleus to the poly(T) capture domain.
11. The method of claim 10 , wherein the nucleic acid analyte is a RNA molecule.
12. The method of claim 10 , wherein the nucleic acid analyte is a DNA molecule.
13. The method of claim 10 , further comprising extending the additional capture probe using the nucleic acid analyte as a template.
14. The method of claim 13 , further comprising releasing the nucleic acid analyte from the additional capture probe.
15. The method of claim 13 , further comprising determining: (i) the sequence of the cellular barcode or a complement thereof and (ii) a sequence of the nucleic acid analyte or a complement thereof.
16. The method of claim 15 , wherein the determining comprises sequencing.
17. The method of claim 1 , wherein the spatial capture probe further comprises a cleavage domain and the incorporating the spatial capture probe into the cell or cell nucleus in (b) comprises cleaving the cleavage domain.
18. The method of claim 17 , wherein the cleavage domain comprises a photocleavable linker.
19. The method of claim 17 , wherein the cleavage domain comprises an enzyme-cleavable linker.
20. The method of claim 1 , wherein the spatial capture probe further comprises a primer binding site and/or a unique molecular identifier.
21. The method of claim 1 , wherein the spatial capture probe further comprises a lipophilic molecule.
22. The method of claim 21 , wherein the lipophilic molecule is selected from the group consisting of: cholesterol, tocopherol, steryl, palmitate, lignoceric acid, and a derivative thereof.
23. The method of claim 1 , further comprising fixing the tissue section.
24. The method of claim 1 , further comprising imaging the tissue section.
25. The method of claim 1 , further comprising staining the tissue section.
26. The method of claim 25 , wherein the staining comprises staining the tissue section with hematoxylin and/or eosin.
27. The method of claim 1 , wherein the tissue section is a fresh-frozen tissue section.
28. A method for spatial identification of a cell nucleus in a tissue section, the method comprising:
a. contacting the tissue section with a bead array comprising a plurality of spatial capture probes, wherein a spatial capture probe of the plurality of spatial capture probes comprises:
i.a spatial barcode, wherein the spatial barcode identifies a location of the spatial capture probe on the bead array; and
ii.a sequence complementary to a capture domain of a cellular capture probe;
b. incorporating the spatial capture probe into the cell nucleus of the tissue section, wherein the spatial capture probe is proximal to the cell nucleus relative to other cell nuclei in the tissue section, thereby generating a spatially-barcoded cell nucleus; and
c. dissociating the tissue section into a plurality of partitions, wherein a partition of the plurality of partitions comprises:
i. the spatially-barcoded cell nucleus; and
ii. a bead coupled to:
1. The cellular capture probe, wherein the cellular capture probe comprises: a cellular barcode, wherein the cellular barcode identifies the partition among the plurality of partitions; and the capture domain,
2. An additional capture probe, wherein the additional capture probe comprises: a sequence of the cellular barcode; and a poly(T) capture domain,
wherein (i) a sequence of the spatial barcode or a complement thereof and (ii) a sequence of the cellular barcode or a complement thereof provide spatial identification of the cell nucleus in the tissue section.
29. The method of claim 28 , further comprising hybridizing the sequence complementary to the capture domain of the spatial capture probe to the capture domain of the cellular capture probe.
30. The method of claim 28 , further comprising hybridizing a nucleic acid analyte from the cell nucleus to the poly(T) capture domain.