Patent ID: 11873483
Assignee: THE BROAD INSTITUTE, INC.
Field: Measurement (Instruments)
Classification: CPC C  G | IPC C  G

Claim 0:
1. A method of identifying whether a target mRNA and a target polypeptide in individual compartments are from the same compartment, comprising:
generating subsamples by segregating a sample, or a portion thereof, into individual compartments, the sample comprising a cell, a population of cells, or an acellular system, wherein each of the individual compartments further comprise:
a first oligonucleotide comprising an origin specific barcode sequence, a unique molecular identifier sequence unique to a target mRNA from the subsamples, and a sequence for binding the target mRNA;
a second oligonucleotide comprising an origin specific barcode sequence and a unique molecular identifier sequence unique to a target polypeptide from the subsamples, and a molecule for capturing the target polypeptide; and
wherein the origin specific barcode sequence of the first oligonucleotide and the origin specific barcode sequence of the second oligonucleotide are the same in each of the individual compartments but differ among the individual compartments;
labeling the target mRNA and the target polypeptide in each of the individual compartments by binding of the first oligonucleotide to the target mRNA and binding of the second oligonucleotide to the target polypeptide, wherein the target mRNA and the target polypeptide in each of the individual compartments are from the acellular system of the subsample or a lysed cell or lysed population of cells of the subsamples within the individual compartments prior to the labeling step;
generating a cDNA product in each of the individual compartments from all or a portion of the labeled target mRNA by introducing reagents for generating the cDNA product into each of the individual compartments such that the origin specific barcode sequence of the first oligonucleotide and the unique molecular identifier sequence unique to the target mRNA is incorporated into the cDNA product;
producing pooled cDNAs by pooling the cDNA product from each of the individual compartments and generating different amplicons comprising the origin specific barcode sequence of the first oligonucleotide and the unique molecular identifier sequence unique to the target mRNA by amplifying the pooled cDNAs, wherein the origin specific barcode sequence of the first oligonucleotide in each of the different amplicons is different;
isolating the labeled target polypeptide labeled in the labeling step from each of the individual compartments and obtaining different cleaved products comprising the origin specific barcode sequence of the second oligonucleotide and the unique molecular identifier sequence unique to the target polypeptide by cleaving the labeled target polypeptide from each of the individual compartments; and
identifying whether a target mRNA and a target polypeptide in the individual compartments are from the same compartment by sequencing of the origin specific barcode sequence of the first oligonucleotide and unique molecular identifier sequence unique to the target mRNA in each of different amplified products and sequencing the origin specific barcode of the second oligonucleotide and unique molecular identifier sequence unique to the target polypeptide in each of the different cleaved products, wherein the origin specific barcode sequence of the first oligonucleotide associated with the target mRNA and the origin specific barcode sequence of the second oligonucleotide associated with target polypeptide are identical indicates that the target mRNA and the target polypeptide in the individual compartments are from the same compartment.