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US 12,180,542 B2Granted
Methods for in SITU transcriptomics and proteomics
AssigneeSingular Genomics Systems, Inc.
InventorsEli N. Glezer, Hu Cang, Zhenmin Hong
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Abstract
Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a cell.
Claims35
A method of monitoring a disease state of a subject;
- said method comprising:
- obtaining a first sample from the subject and obtaining a second sample from the subject at a later time, wherein the first sample and the second sample each comprise a tissue or cell comprising a plurality of proteins associated with the disease state;
- followed by
- concurrently contacting both the first sample and the second sample with a plurality of specific binding reagents;
- binding a specific binding reagent to a protein associated with the disease state in the first sample, and binding a specific binding reagent to a protein associated with the disease state in the second sample, wherein each specific binding reagent comprises an oligonucleotide barcode from a known set of oligonucleotide barcodes associated with each protein;
- and
- sequencing each oligonucleotide barcode in said tissue or in or on said cell.
4 more elements
A method of monitoring a disease state of a subject;
- said method comprising:
- obtaining a first sample from the subject and obtaining a second sample from the subject at a later time, wherein the first sample and the second sample each comprise a tissue or cell comprising one or more nucleic acid molecules associated with the disease state and one or more proteins associated with the disease state;
- followed by
- contacting both the first sample and the second sample with a plurality of circularizable probes and binding a circularizable probe to a nucleic acid molecule associated with the disease state in the first sample and binding a circularizable probe to a nucleic acid molecule associated with the disease state in the second sample, wherein each circularizable probe comprises a sequence complementary to the nucleic acid molecule associated with a disease state, a primer binding sequence, and a barcode sequence;
- amplifying each circularizable probe to generate amplification products comprising the barcode sequence, or a complement thereof;
- and
- sequencing the amplification products in or on said tissue or cell;
- and
- concurrently contacting both the first sample and the second sample with a plurality of specific binding reagents and binding a specific binding reagent to a protein associated with the disease state, wherein each specific binding reagent comprises an oligonucleotide barcode;
- and
- sequencing each oligonucleotide barcode in or on said tissue or cell.
8 more elements
A kit, comprising:
- i) a solid support;
- ii) a first antibody-oligonucleotide conjugate, comprising a first oligonucleotide barcode and a second antibody-oligonucleotide conjugate comprising a second oligonucleotide barcode, wherein the first and second oligonucleotide barcodes comprise different sequences;
- iii) a first oligonucleotide probe complementary to the first oligonucleotide barcode comprising a first primer binding sequence and a second oligonucleotide probe complementary to the second oligonucleotide barcode comprising a second primer binding sequence;
- and
- iv) a first primer comprising a sequence complementary to the first primer binding sequence and a second primer comprising a sequence complementary to the second primer binding sequence.
2 more elements
A plurality of samples from a subject, wherein each sample comprises a tissue or cell and is obtained from the subject at a different time, each sample comprising:
- a) one or more nucleic acid molecules each bound to a polynucleotide probe in said tissue or cell, wherein the polynucleotide probe is a circular polynucleotide comprising a first primer binding sequence and a first barcode sequence, wherein the first barcode sequence is from a known set of barcodes associated with the bound nucleic acid molecule;
- and
- b) one or more proteins each bound to a specific binding reagent in said tissue or in or on said cell, wherein the specific binding reagent comprises an oligonucleotide comprising a second primer binding sequence and a second barcode sequence associated with the specific binding reagent, wherein the second barcode sequence is from a known set of barcodes associated with the bound protein.
A method of monitoring samples, said method comprising:
- depositing a first sample at a first location on a solid support and depositing a second sample at a second location on the solid support, wherein the first sample comprises a plurality of cells and the second sample comprises a plurality of cells;
- fixing the plurality of cells of the first sample;
- fixing the plurality of cells of the second sample at a later time;
- contacting the first sample and the second sample with a plurality of specific binding reagents;
- binding a specific binding reagent to a protein in the first sample, and binding a specific binding reagent to a protein in the second sample, wherein each specific binding reagent comprises an oligonucleotide barcode from a known set of oligonucleotide barcodes;
- and
- sequencing each oligonucleotide barcode in each sample.
4 more elements
Dependencies are inferred from the claim text.