US 12,129,463 B2
Methods and kits using nucleic acid encoding and/or label
Mark S. Chee, Encinitas, CA (US); Kevin L. Gunderson, San Diego, CA (US); Michael Phillip Weiner, San Diego, CA (US); Lei Shi, San Diego, CA (US); and Norihito Muranaka, San Diego, CA (US)
Assigned to Encodia, Inc., San Diego, CA (US)
Filed by Encodia, Inc., San Diego, CA (US)
Filed on Mar. 22, 2023, as Appl. No. 18/125,075.
Application 18/125,075 is a continuation of application No. 16/760,032, previously published as PCT/US2018/058583, filed on Oct. 31, 2018.
Claims priority of provisional application 62/582,916, filed on Nov. 7, 2017.
Claims priority of provisional application 62/579,840, filed on Oct. 31, 2017.
Prior Publication US 2023/0340458 A1, Oct. 26, 2023
Int. Cl. C12N 15/10 (2006.01); C12Q 1/6804 (2018.01); G01N 33/68 (2006.01)
CPC C12N 15/1065 (2013.01) [C12Q 1/6804 (2013.01); G01N 33/68 (2013.01); G01N 2458/10 (2013.01)] 15 Claims
OG exemplary drawing
 
1. A method for assaying interactions between a set of polypeptides from different biological samples and a library of binding agents, comprising:
(a) generating a set of immobilized polypeptides by
(i) labeling polypeptides from different biological samples with recording tags each comprising a polypeptide-specific barcode and a sample-specific barcode, thereby generating polypeptide-recording tag conjugates from different biological samples,
(ii) pooling the polypeptide-recording tag conjugates from different biological samples together; and
(iii) immobilizing the polypeptide-recording tag conjugates from different biological samples on a plurality of solid supports,
wherein for each solid support, multiple molecules of different polypeptides immobilized on the solid support are spatially separated by at least 50 nm;
(b) contacting:
the set of immobilized polypeptides with
the library of binding agents, wherein each binding agent from the library of binding agents comprises a polypeptide or an aptamer, and is associated with a nucleic acid coding tag that provides identifying information regarding the binding agent;
(c) following binding of one or more binding agents to one or more immobilized polypeptides, allowing transfer of identifying information regarding the one or more binding agent by primer extension and/or ligation between
nucleic acid coding tag(s) associated with the one or more binding agents and
nucleic acid recording tag(s) associated with the one or more immobilized polypeptides,
wherein the transfer of identifying information generates extended nucleic acid recording tag(s) associated with the one or more immobilized polypeptides and/or extended nucleic acid coding tag(s) associated with the one or more binding agents; and
(d) analyzing the extended nucleic acid recording tag(s) and/or extended nucleic acid coding tag(s) by nucleic acid sequencing to obtain the identifying information regarding the one or more binding agents and the identifying information regarding the one or more polypeptides including their sample origin,
thereby assaying the interactions between the set of polypeptides and the library of binding agents, and creating a polypeptide-agent binding matrix having size of at least 106.