Abstract: Disclosed herein are methods for analyzing one or more analytes of a cell by performing single-cell analysis. In one scenario, the one or more analytes are located on a surface of the cell. In one scenario, the one or more analytes are located internally within the cell. In one scenario, the one or more analytes include proteins located on a surface of the cell and located internally within the cell.

Abstract: Provided herein are methods and systems for the simultaneous targeted detection and sequencing of DNA, RNA, and Protein. In typical embodiments, the DNA, RNA, and Proteins are detected, characterized, and sequenced using just a single mammalian cell. One embodiment of detecting and characterizing DNA, RNA, or protein from a mammalian cell includes encapsulating a single cell in a drop and performing a protease digest on the encapsulated cell drop, performing a reverse transcriptase reaction; performing a droplet merger with barcoding PCR reagents and barcoding beads; performing a PCR reaction to attach the cell barcodes to the DNA targeted amplicons, RNA targeted amplicons, and protein tag amplicons, where all amplicons from the same emulsion contain the same cell barcode; and detecting and characterizing a DNA, RNA, or protein amplicon by sequencing the cell barcode incorporated into each amplicon.

Abstract: Single-cell analysis of a population of cells reveals cellular genotypes (e.g., single nucleotide variants and copy number variations) and phenotypes (e.g., protein expression) of individual cells. In one scenario, individual cells can be classified according to their respective genotypes and phenotypes. In one scenario, genotypes and phenotypes of all cells in the population are informative for identifying subpopulations of cells, thereby revealing intra-population heterogeneity. The identification of subpopulations of cells is informative for improving the understanding of cellular biology, especially in the context of diseases such as cancer, and is further informative for the better design of diagnostics and therapies.

Abstract: Single-cell analysis using combined RNA sequencing of RNA transcripts and DNA sequencing of chromatin-accessible DNA is performed to determine trajectories of single cells. Individual cells are encapsulated and lysed using reagents that do not include proteases or transposases. Cell lysates include RNA transcripts and packaged DNA (e.g., DNA packaged as chromatin) Segments of DNA in the packaged DNA are primed, amplified, and sequenced to generate sequence reads of the chromatin-accessible DNA. RNA transcripts are reverse transcribed to generate cDNA which is then primed, amplified, and sequenced to generate sequence reads. Sequence reads from the RNA-seq and DNA-seq reveal different states of cells and therefore, are useful for predicting cell trajectories.

Abstract: Provided herein are methods and systems for the simultaneous targeted detection and sequencing of DNA, RNA, and Protein. In typical embodiments, the DNA, RNA, and Proteins are detected, characterized, and sequenced using just a single mammalian cell. One embodiment of detecting and characterizing DNA, RNA, or protein from a mammalian cell includes encapsulating a single cell in a drop and performing a protease digest on the encapsulated cell drop, performing a reverse transcriptase reaction; performing a droplet merger with barcoding PCR reagents and barcoding beads; performing a PCR reaction to attach the cell barcodes to the DNA targeted amplicons, RNA targeted amplicons, and protein tag amplicons, where all amplicons from the same emulsion contain the same cell barcode; and detecting and characterizing a DNA, RNA, or protein amplicon by sequencing the cell barcode incorporated into each amplicon.

Abstract: Provided herein are methods for detection and characterization of a target nucleic acid from a single cell. One embodiment is a method for detection of a BCR-ABL gene fusion in a nucleic acid sample from a single cell having or suspected of having a BCR-ABL fusion transcript. One preferred implementation of the invention includes providing a nucleic acid amplification primer set complementary to a target nucleic acid suspected of having a BCR-ABL fusion transcript. In some embodiments, one or both primers of the nucleic acid amplification primer set have a barcode identification sequence. Also provided are methods for the detection of an AML tumor, methods are used for the detection of a leukemia, for the detection of a myeloid leukemia, and to determine the prognosis of a patient suspected of having a BCR-ABL fusion transcript.

Abstract: Provided herein are methods and systems for the simultaneous targeted detection and sequencing of DNA, RNA, and Protein. In typical embodiments, the DNA, RNA, and Proteins are detected, characterized, and sequenced using just a single mammalian cell. One embodiment of detecting and characterizing DNA, RNA, or protein from a mammalian cell includes encapsulating a single cell in a drop and performing a protease digest on the encapsulated cell drop, performing a reverse transcriptase reaction; performing a droplet merger with barcoding PCR reagents and barcoding beads; performing a PCR reaction to attach the cell barcodes to the DNA targeted amplicons, RNA targeted amplicons, and protein tag amplicons, where all amplicons from the same emulsion contain the same cell barcode; and detecting and characterizing a DNA, RNA, or protein amplicon by sequencing the cell barcode incorporated into each amplicon.

Abstract: Provided herein are methods and systems for identifying and characterizing proteins, in particular cell surface proteins, of different cell types at the single-cell level. Also provided are methods and systems for distinguishing cells by their protein expression profiles. Further, methods and systems to quantitate and characterize proteins in single cells at ultrahigh throughput are provided. The methods and systems provided herein are able to sensitively profile all epitopes in a proteome of a single cell.

Abstract: Provided herein are methods for detection and characterization of a target nucleic acid from a single cell. Some embodiments highlight the capability of identifying the biologically relevant variants at the moment of the diagnosis, but also how the treatment positively select resistant cellular clones based on the mutation signature. This positions the Tapestri™ platform described herein as the only tool available to study how genetic variants co-exist and which combinations are sensitive and resistant to certain treatments.

Abstract: An instrument module “DualPlay” housing system includes a first instrument module which is constructed from a measurement board enclosed by a first protective instrument module casing. The first instrument module is additionally enclosed in a main storage compartment of a housing. Additional instrument modules are enclosed in additional housings. Securing sections at the tops and bottoms of the housings secure the housings in a vertical stacked configuration.

Abstract: A clamshell housing is used in a stand-alone configuration of “DualPlay” instrument modules. The housing comprises first and second sections pivotally connected by a hinge mechanism at a hinge end of the clamshell housing that allows rotation of the first and second sections relative to one other between an open and closed position. An open end of the clamshell housing is opposite to the hinge end. A sliding-fastener bumper section slides over the open end and secures the sections in the closed position. A main storage compartment is formed by the first and second sections when in the closed position and serves to hold the instrument module.