Method for resetting an array
Provided herein are methods for resetting an array to which a biological sample has been applied that include treating the array with a set of biological sample removal conditions.
1. A method for resetting an array, the method comprising:
(a) applying an animal tissue section to an array, wherein the array comprises a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises a capture domain that binds to a nucleic acid from the animal tissue section; and
(b) treating the array with a set of biological sample removal conditions, such that the animal tissue section is substantially removed from the array, wherein prior to said treating the array with the set of biological sample removal conditions, the animal tissue section applied on the array is permeabilized and no enzymatic extension reaction has been performed on the capture probes, and said treating the array with the set of biological sample removal conditions comprises treating the array with a base having a particular concentration, wherein the base is a base selected from potassium hydroxide, sodium hydroxide, and a combination thereof,
thereby resetting the array.
2. The method of claim 1 , wherein the array is a tissue optimization array or a spatial array.
3. The method of claim 1 , wherein the nucleic acid is mRNA.
4. The method of claim 1 , wherein the nucleic acid is DNA.
5. The method of claim 1 , wherein said treating the array with the set of biological sample removal conditions further comprises washing the array one or more times.
6. The method of claim 5 , wherein said treating the array with the set of biological sample removal conditions further comprises washing the array with a buffer one or more times.
7. The method of claim 6 , wherein the buffer is selected from the group consisting of: Tris, phosphate buffered saline (PBS), HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), TES (2-[(2-Hydroxy-1, 1-bis(hydroxymethyl)ethyl)amino]ethanesulfonic acid), and combinations thereof.
8. The method of claim 5 , wherein said treating the array with the set of biological sample removal conditions further comprises drying the array.
9. The method of claim 5 , wherein said treating the array with the set of biological sample removal conditions comprises, sequentially, treating the array with a proteinase, washing the array with water, treating the array with the base, washing the array with a buffer, and washing the array with water, and optionally, drying the array.
10. The method of claim 9 , wherein the proteinase is proteinase K.
11. The method of claim 5 , wherein the method further comprises, between step (a) and step (b), a step of identifying whether the animal tissue section has been applied to the array incorrectly or does not contain a region of interest.
12. The method of claim 11 , wherein said identifying whether the animal tissue section has been applied to the array incorrectly or does not contain a region of interest comprises: identifying whether one or more fiducial markers on the array is obscured by the animal tissue section, identifying whether the animal tissue section is folded, identifying whether the animal tissue section is torn or damaged, identifying whether the animal tissue section overlaps with a different animal tissue section if a plurality animal tissue sections is applied to the array, imaging the animal tissue section after staining or immunofluorescence staining the array, or a combination thereof.
13. The method of claim 5 , wherein the array is a spatial array and the method further comprises after step (b):
(c) contacting the spatial array with a different animal tissue section.
14. The method of claim 5 , wherein the array is a tissue optimization array and the method further comprises after step (b):
(c) contacting the tissue optimization array with a different animal tissue section.
15. A method for resetting an array to which an animal tissue section has been applied, the method comprising:
treating the array with a set of biological sample removal conditions, such that the animal tissue section is substantially removed from the array, wherein the array comprises a plurality of capture probes,
wherein a capture probe of the plurality of capture probes comprises a capture domain that binds specifically to a nucleic acid from the animal tissue section, and
wherein prior to said treating the array with the set of biological sample removal conditions, the animal tissue section applied on the array is permeabilized and no enzymatic extension reaction has been performed on the capture probes, and said treating the array with the set of biological sample removal conditions comprises treating the array with a base having a particular concentration, wherein the base is a base selected from potassium hydroxide, sodium hydroxide, and a combination thereof,
thereby resetting the array.
16. The method of claim 15 , wherein the array is a tissue optimization array or a spatial array.
17. The method of claim 15 , wherein the nucleic acid is mRNA.
18. The method of claim 15 , wherein the nucleic acid is DNA.
19. The method of claim 15 , wherein said treating the array with the set of biological sample removal conditions further comprises washing the array one or more times.
20. The method of claim 15 , wherein said treating the array with the set of biological sample removal conditions further comprises washing the array with a buffer one or more times.
21. The method of claim 20 , wherein the buffer is selected from the group consisting of: Tris, phosphate buffered saline (PBS), HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), TES (2-[(2-Hydroxy-1, 1-bis(hydroxymethyl)ethyl)amino]ethanesulfonic acid), and combinations thereof.
22. The method of claim 15 , wherein said treating the array with the set of biological sample removal conditions further comprises drying the array.
23. The method of claim 15 , wherein said treating the array with the set of biological sample removal conditions comprises, sequentially, treating the array with a proteinase, washing the array with water, treating the array with the base, washing the array with a buffer, and washing the array with water, and optionally, drying the array.
24. The method of claim 23 , wherein the proteinase is proteinase K.
25. The method of claim 15 , wherein the method further comprises, between step (a) and step (b), a step of identifying whether the animal tissue section has been applied to the array incorrectly or does not contain a region of interest.
26. The method of claim 25 , wherein said identifying whether the animal tissue section has been applied to the array incorrectly or does not contain a region of interest comprises: identifying whether one or more fiducial markers on the array is obscured by the animal tissue section, identifying whether the animal tissue section is folded, identifying whether the animal tissue section is torn or damaged, identifying whether the animal tissue section overlaps with a different animal tissue section if the different animal tissue section is also applied to the array, imaging the animal tissue section after staining or immunofluorescence staining the array, or a combination thereof.
27. The method of claim 15 , wherein the array is a spatial array and the method further comprises after said treating the array with a set of biological sample removal conditions:
contacting the spatial array with a different animal tissue section.
28. The method of claim 15 , wherein the array is a tissue optimization array and the method further comprises after said treating the array with a set of biological sample removal conditions:
contacting the tissue optimization array with a different animal tissue section.