Spatial molecular analysis of tissue

1. A method of spatially mapping a tissue sample, the method comprising the steps of:

providing a microarray having a plurality of wells, wherein adjacent wells are separated by a shearing surface;

overlaying said microarray with a tissue sample;

applying a deformable substrate to an upper surface of said tissue sample;

applying a force to said deformable substrate, thereby forcing underlying tissue sample into said plurality of wells;

shearing said tissue sample along said shearing surface into a plurality of tissue sample islands, with each unique tissue sample island positioned in a unique well; and

imaging or quantifying said plurality of tissue sample islands, thereby generating a spatial map of said tissue sample.

2. The method of claim 1 , further comprising the step of pre-spotting or printing one or more molecules on a surface of the plurality of wells.

3. The method of claim 1 , further comprising the step of removing said deformable substrate before said imagining or quantifying step and applying a reagent for use in said imaging or quantifying step.

4. The method of claim 3 , wherein said reagent comprises a plurality of reagents for nucleic acid amplification, the method further comprising the step of amplifying nucleic acid in each of said plurality of wells using a nucleic acid amplification technique, thereby generating a plurality of amplified products.

5. The method of claim 4 , wherein said imaging comprises analyzing said plurality of amplified products, thereby generating a spatial gene analysis of said tissue sample.

6. The method of claim 1 , wherein said step of applying a force to said deformable substrate is performed by spinning said microarray with said tissue sample and deformable substrate in a centrifuge.

7. The method of claim 1 , wherein each of said wells has a volume of less than or equal to 1000 pL; a cross-sectional dimension of less than or equal to 1 mm, or a maximum depth of less than or equal to 1 mm.

8. The method of claim 1 , wherein said tissue sample is a histological tissue section.

9. The method of claim 1 , wherein said tissue sample has an average thickness of less than or equal to 20 μm.

10. The method of claim 1 , wherein said tissue sample is cryopreserved.

11. The method of claim 1 , wherein said deformable substrate comprises a polymer, wherein after said applied force is removed, said deformable layer exits said wells and relaxes back to a rest state, and the plurality of tissue sample islands remain within said plurality of wells.

12. The method of claim 11 , wherein said polymer is polymethylsiloxane (PDMS), SU-8, polyethylene glycol (PEG), a photoresist, a PEG-based polymer or any combination thereof.

13. The method of claim 1 , further comprising the step of delivering one or more reagents and/or molecules to the plurality of wells before the step of overlaying said microarray with the tissue sample, wherein the one or more reagents and/or molecules are useful for the imaging or quantifying step.

14. The method of claim 1 , further comprising the step of delivering one or more reagents and/or molecules to the plurality of wells after the shearing step, wherein the one or more reagents and/or molecules are useful for the imaging or quantifying step and the delivering is by one or more than one delivery application steps.

15. The method of claim 1 , further comprising the step of processing said tissue sample islands by:

removing said deformable substrate;

applying reagents used to image and/or quantify the tissue sample islands to each of said wells, wherein the applying step comprises:

covering the wells with liquid reagent, wherein the liquid reagent enters the wells by capillary action;

immersing the wells with liquid reagent in an inert covering fluid having a density that is less than the liquid reagent density, thereby enveloping each well containing a tissue sample island and liquid reagent; and

removing excess reagent by forcing a gas over the wells, thereby avoiding cross-talk between different wells.

16. The method of claim 1 , further comprising the step of fixing and permeabilizing said tissue sample islands.

17. The method of claim 4 , wherein said nucleic acid amplification technique comprises PCR.

18. The method of claim 4 , wherein said amplification method is an isothermal amplification method.

19. The method of claim 1 , comprising fluorescent imaging.

20. The method of claim 1 , further comprising adding an optically detectable dye or particle to each of said plurality of wells.

21. The method of claim 1 , wherein the imaging or quantifying step comprises quantifying an electrical parameter in each of the wells.

22. The method of claim 1 applied to one or more of:

an on-chip spatial gene expression analysis;

on-chip spatial RNA sequence analysis;

on-chip spatial methylation analysis;

on-chip gene mutation analysis;

on-chip copy number variation analysis; or

on-chip insertion and deletion analysis.

23. The method of claim 1 , applied to pathogen detection, tissue functionality assessment, or pathological diagnostics.

24. The method of claim 1 , wherein the microarray comprises greater than 500 wells.

25. A method for generating a pixelated, spatially-preserved tissue sample comprising the steps of:

providing a microarray having a plurality of wells, wherein at least a portion of each edge of said wells is a shearing surface;

providing a tissue sample in contact with each of said wells;

overlaying a deformable layer on said tissue sample;

applying a force upon said deformable layer, thereby forcing said deformable layer and said tissue sample into said plurality of wells and shearing said tissue sample into a plurality of tissue sample islands positioned in said plurality of wells; and

relaxing said force, thereby removing said deformable layer from said plurality of wells, while maintaining said plurality of tissue sample islands positioned in said plurality of wells, thereby generating a pixelated, spatially-preserved tissue sample.