US 12,168,226 B2
High resolution spatial genomic analysis of tissues and cell aggregates
Jason A. A. West, Chapel Hill, NC (US); and Kyle Hukari, Foster City, CA (US)
Assigned to BioSkryb Genomics, Inc., Durham, NC (US)
Appl. No. 16/342,758
Filed by BioSkryb Genomics, Inc., Durham, NC (US)
PCT Filed Oct. 17, 2017, PCT No. PCT/US2017/056865
§ 371(c)(1), (2) Date Apr. 17, 2019,
PCT Pub. No. WO2018/075436, PCT Pub. Date Apr. 26, 2018.
Prior Publication US 2019/0262831 A1, Aug. 29, 2019
Int. Cl. C12Q 1/6816 (2018.01); B01L 3/00 (2006.01); C12Q 1/68 (2018.01); C12Q 1/6851 (2018.01); C12Q 1/6853 (2018.01); C40B 20/02 (2006.01); C40B 20/04 (2006.01); C40B 40/06 (2006.01); C40B 40/10 (2006.01); B01L 7/00 (2006.01)
CPC B01L 3/502715 (2013.01) [B01L 3/5027 (2013.01); B01L 3/502753 (2013.01); C12Q 1/68 (2013.01); C12Q 1/6816 (2013.01); C12Q 1/6851 (2013.01); C12Q 1/6853 (2013.01); C40B 20/02 (2013.01); C40B 20/04 (2013.01); C40B 40/06 (2013.01); C40B 40/10 (2013.01); B01L 7/525 (2013.01); B01L 2200/0647 (2013.01); B01L 2300/021 (2013.01); B01L 2300/0645 (2013.01); B01L 2300/0681 (2013.01); B01L 2300/0819 (2013.01); B01L 2300/0861 (2013.01); B01L 2300/0887 (2013.01); B01L 2300/1827 (2013.01); B01L 2400/0421 (2013.01)] 12 Claims
 
1. A method for spatial analysis comprising:
(a) providing or obtaining an integrated system comprising:
(i) a first surface comprising a porous cellular support;
(ii) a second surface comprising a tile array of barcoded oligonucleotides, wherein the tile array comprises a plurality of regions defined on a plane and a barcoded oligonucleotide of the tile array comprises a regional barcode shared between barcoded oligonucleotides of a first region of the tile array and different among the different regions of the tile array;
(iii) a chamber defined between the first surface and the second surface comprising a cellular sample affixed to the porous cellular support and in direct fluid communication with the tile array via fluid transport through pores of the porous cellular support; and,
(iv) one or more electrodes for generating a voltage gradient between the porous cellular support and the tile array of barcoded oligonucleotides for generating perpendicular fluid flow therebetween and through the chamber;
(b) liberating a nucleic acid molecule from a cell of the cellular sample;
(c) translocating the liberated nucleic acid in a direction essentially perpendicular to the porous cellular support substrate, through pores of the porous cellular support substrate toward the tile array of barcoded oligonucleotides by applying the voltage gradient;
(d) hybridizing the liberated nucleic acid to a barcoded oligonucleotide of the tile array, wherein the regional barcode of the barcoded oligonucleotide identifies the region of the cell in the cellular sample;
(e) amplifying the nucleic acid to generate a plurality of amplification products therefrom; and
(f) identifying the region of the cell using the regional barcode.