US 11,739,381 B2
Multiplex capture of gene and protein expression from a biological sample
Jennifer Chew, Pleasanton, CA (US); Joseph Francis Shuga, Pleasanton, CA (US); Patrick Roelli, Stockholm (SE); Denise Cheung, Pleasanton, CA (US); Alexander Hermes, Pleasanton, CA (US); Yifeng Yin, Pleasanton, CA (US); Naishitha Anaparthy, Pleasanton, CA (US); Ryo Hatori, Pleasanton, CA (US); Marlon Stoeckius, Stockholm (SE); Rapolas Spalinskas, Pleasanton, CA (US); Anna-Maria Katsori, Stockholm (SE); Cedric Uytingco, Pleasanton, CA (US); Mesruh Turkekul, Stockholm (SE); David Sukovich, Pleasanton, CA (US); Christina Galonska, Stockholm (SE); Aleksandra Jurek, Pleasanton, CA (US); and Octavian Marian Bloju, Stockholm (SE)
Assigned to 10x Genomics, Inc., Pleasanton, CA (US)
Filed by 10x Genomics, Inc., Pleasanton, CA (US)
Filed on Jul. 18, 2022, as Appl. No. 17/867,223.
Application 17/867,223 is a continuation of application No. PCT/US2022/020985, filed on Mar. 18, 2022.
Claims priority of provisional application 63/311,703, filed on Feb. 18, 2022.
Claims priority of provisional application 63/270,230, filed on Oct. 21, 2021.
Claims priority of provisional application 63/252,335, filed on Oct. 5, 2021.
Claims priority of provisional application 63/245,697, filed on Sep. 17, 2021.
Claims priority of provisional application 63/214,058, filed on Jun. 23, 2021.
Claims priority of provisional application 63/162,870, filed on Mar. 18, 2021.
Prior Publication US 2022/0389504 A1, Dec. 8, 2022
Int. Cl. C12Q 1/6874 (2018.01); C12N 15/10 (2006.01); C12Q 1/6837 (2018.01)
CPC C12Q 1/6874 (2013.01) [C12N 15/1065 (2013.01); C12Q 1/6837 (2013.01)] 23 Claims
OG exemplary drawing
 
1. A method for determining the spatial location of a nucleic acid and a protein from a biological sample comprising:
a) providing a spatial array comprising a first and second plurality of capture probes wherein each of the first and second plurality of capture probes comprises a spatial barcode and a capture domain,
b) contacting the biological sample with
(i) a plurality of analyte capture agents, wherein an analyte capture agent comprises an analyte binding moiety and an oligonucleotide comprising an analyte binding moiety barcode and an analyte capture sequence, wherein the analyte capture sequence comprises a sequence complementary to a second plurality of capture domains, and
(ii) a plurality of templated ligation probe pairs, wherein one of the templated ligation probes in the probe pair comprises a sequence complementary to a first plurality of capture domains,
c) binding the analyte binding moiety of the analyte capture agent to a target protein,
d) hybridizing the templated ligation probe pairs to a target nucleic acid and ligating the probe pairs to produce ligation products,
e) hybridizing the ligation products to the first plurality of capture domains and the analyte capture sequences of the bound analyte capture agents to the second plurality of capture domains on the spatial array, and
f) determining the sequence or a portion thereof of (i) the ligation product, or a complement thereof, (ii) the spatial barcode of the capture probe hybridized to the ligation product, or a complement thereof, (iii) the analyte binding moiety barcode of the analyte capture agent bound to the target protein, or a complement thereof, and (iv) the spatial barcode of the capture probe hybridized to the oligonucleotide comprising the analyte binding moiety barcode the analyte capture sequence, thereby determining the spatial location of the nucleic acid and the protein from the biological sample.