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: Disclosed herein is a single-cell analysis workflow involving whole genome amplification for developing single-cell whole genome DNA libraries. The single-cell analysis workflow involves encapsulating and lysing cells in individual droplets and releasing genomic DNA from chromatin within the droplet. Transposases access the released genomic DNA and insert adaptor sequences into the cleaved nucleic acid fragments, thereby generating tagmented genomic DNA fragments that span the whole genome. Tagmented genomic DNA undergo nucleic acid amplification and sequencing for generating single-cell whole genome DNA libraries.

Abstract: Digestible primers are incorporated into single cell analysis workflows to reduce and/or eliminate primer byproducts and misprimed nucleic acids. Specifically, digestible primers can participate in a first reaction, such as reverse transcription of RNA transcripts to generate cDNA, but digestible primers are digested to prevent them from participating in subsequent reactions, such as nucleic acid amplification. For example, digestible primers can include a primer with one or more ribonucleotide nucleobases, a primer with uracil bases, a primer with deoxyuridine sequences, or a primer with ribouridine sequences. Such primers can then be digested (e.g., enzymatically digested) to remove them from interfering in subsequent nucleic acid amplification reactions.

Abstract: Provided are methods, as well as compositions, kits, and systems for preparing optimized control nucleic acids (polynucleotides) having reduce nucleic acid damage. Provided nucleic acid compositions provide reduced artifacts as compared to nucleic acid compositions prepared by conventional methods. Provided compositions are useful control in a variety of applications, including, but not limited to sequencing workflows to effectively monitor sensitivity, accuracy and/or precision of data.

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: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.

Abstract: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.

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: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.

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: Provided herein are methods for detection of a target nucleic acid from a single cell. Preferred embodiments of the method include selecting one or more target nucleic acid sequence of interest in an individual cell, where the target nucleic acid sequence is typically complementary to cellular DNA, including a genomic DNA, and an RNA in a cell. A cell sample is provided, and in preferred embodiments the sample is from a single cell. The cell is lysed and in a single reaction both DNA and RNA can be detected without sub-dividing the sample. This can be accomplished by providing nucleic acid amplification primer sets complementary to one or more target nucleic acid, and in particular primer sets that selectively amplify particular target nucleic acids or amplicons in an amplification reaction. Also provided are methods of primer design for these methods and apparatus and system used to perform the methods.

Abstract: Provided are methods, as well as compositions, kits, and systems for preparing optimized control nucleic acids (polynucleotides) having reduce nucleic acid damage. Provided nucleic acid compositions provide reduced artifacts as compared to nucleic acid compositions prepared by conventional methods. Provided compositions are useful control in a variety of applications, including, but not limited to sequencing workflows to effectively monitor sensitivity, accuracy and/or precision of data.

Abstract: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.

Abstract: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.

Abstract: Methods are provided for tagging, characterizing and sorting double-stranded biomolecules while maintaining the integrity of the biomolecules.