US 11,952,626 B2
Probe-based analysis of nucleic acids and proteins
Katherine Pfeiffer, San Francisco, CA (US); Andrew Scott Kohlway, Dublin, CA (US); Andrew John Hill, Seattle, WA (US); and Paul Eugene Lund, San Leandro, CA (US)
Assigned to 10X GENOMICS, INC., Pleasanton, CA (US)
Filed by 10x Genomics, Inc., Pleasanton, CA (US)
Filed on Aug. 22, 2023, as Appl. No. 18/236,540.
Application 18/236,540 is a continuation of application No. PCT/US2022/017377, filed on Feb. 22, 2022.
Claims priority of provisional application 63/251,446, filed on Oct. 1, 2021.
Claims priority of provisional application 63/235,487, filed on Aug. 20, 2021.
Claims priority of provisional application 63/196,834, filed on Jun. 4, 2021.
Claims priority of provisional application 63/152,709, filed on Feb. 23, 2021.
Prior Publication US 2023/0399691 A1, Dec. 14, 2023
Int. Cl. C12Q 1/68 (2018.01); C12Q 1/6818 (2018.01); C12Q 1/6874 (2018.01)
CPC C12Q 1/6874 (2013.01) [C12Q 1/6818 (2013.01); C12Q 2600/16 (2013.01)] 30 Claims
OG exemplary drawing
 
1. A method of analyzing a cell, comprising:
(a) providing a sample comprising a cell, wherein the cell comprises:
(i) a feature, wherein the feature comprises a protein, a peptide, a lipid, or a carbohydrate; and
(ii) a nucleic acid molecule; and
(b) contacting the cell with a feature binding group and coupling the feature binding group to the feature, wherein the feature binding group comprises an oligonucleotide comprising a feature nucleic acid sequence that identifies the feature binding group;
(c) hybridizing a first nucleic acid probe to the nucleic acid molecule; wherein the first nucleic acid probe comprises (i) a hybridizing sequence that hybridizes to a first target sequence of the nucleic acid molecule and (ii) a non-hybridizing sequence;
(d) using the feature nucleic acid sequence and a first barcode molecule comprising a first barcode sequence to generate a first barcoded nucleic acid molecule comprising (i) the feature nucleic acid sequence or reverse complement thereof, and (ii) the first barcode sequence or reverse complement thereof; and
(e) using the non-hybridizing sequence and a second barcode molecule comprising a second barcode sequence to generate a second barcoded nucleic acid molecule comprising (i) the first target sequence or reverse complement thereof and (ii) the second barcode sequence or reverse complement thereof.