Abstract: Disclosed herein include systems, methods, compositions, and kits for quantitative analysis of a plurality of cellular component targets of cells of interest. In some embodiments, an oligonucleotide associated with a cellular component-binding reagent (e.g., an antibody) is associated with one or more detectable moieties (e.g., luminescent moieties, fluorescent moieties, a phosphorescent moieties). In some embodiments, the presence of the detectable moiety in the binding reagent oligonucleotide enables the cellular component-binding reagent to be employed for both fluorescence analysis (e.g., cell sorting) and sequence analysis (e.g., protein expression profiling).

Abstract: Disclosed herein include systems, methods, compositions, and kits for performing targeted single cell mRNA sequencing assays. Capture oligonucleotides capable of specifically binding to target nucleic acid species are provided in some embodiments. Depletion oligonucleotides capable of specifically binding to undesirable nucleic acid species are provided in some embodiments. The method can comprise random priming and extension of barcoded transcripts followed by one or more enrichment and/or depletion steps using said capture oligonucleotides and/or depletion oligonucleotides. Immune repertoire profiling methods are also provided in some embodiments.

Abstract: Disclosed herein include systems, methods, compositions, and kits for determining the expression of highly expressed proteins and lowly expressed proteins. In some embodiments, primers allowing generation of separate libraries for abundant AbSeq protein profiling oligonucleotides and scarce AbSeq protein profiling oligonucleotides are provided.

Abstract: Disclosed herein include systems, methods, compositions, and kits for quantitative analysis of a plurality of cellular component targets of cells of interest. In some embodiments, an oligonucleotide associated with a cellular component-binding reagent (e.g., an antibody) is associated with one or more detectable moieties (e.g., luminescent moieties, fluorescent moieties, a phosphorescent moieties). In some embodiments, the presence of the detectable moiety in the binding reagent oligonucleotide enables the cellular component-binding reagent to be employed for both fluorescence analysis (e.g., cell sorting) and sequence analysis (e.g., protein expression profiling).

Abstract: Disclosed herein include systems, methods, compositions, and kits for labeling nucleic acid targets in a sample. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3? end and are subsequently barcoded on the 5? end following a template switching reaction and intermolecular and/or intramolecular hybridization and extension. 5?- and/or 3?-barcoded nucleic acid targets can serve as templates for amplification reactions and/or random priming and extension reactions to generate a sequencing library. The method can comprise generating a full-length sequence of the nucleic acid target by aligning a plurality of sequencing reads. Immune repertoire profiling methods are also provided in some embodiments.

Abstract: Disclosed herein include systems, methods, compositions, and kits for determining the expression of highly expressed proteins and lowly expressed proteins. In some embodiments, primers allowing generation of separate libraries for abundant AbSeq protein profiling oligonucleotides and scarce AbSeq protein profiling oligonucleotides are provided.

Abstract: Disclosed herein include systems, methods, compositions, and kits suitable for the use of dextramers in single cell analysis. In some embodiments, one or more primers allowing generation of separate libraries for proteins (e.g., antibodies) and for dextramers are used.

Abstract: Disclosed herein include systems, methods, compositions, and kits for determining the expression of highly expressed proteins and lowly expressed proteins. In some embodiments, primers allowing generation of separate libraries for abundant AbSeq protein profiling oligonucleotides and scarce AbSeq protein profiling oligonucleotides are provided.

Abstract: Disclosed herein include systems, methods, compositions, and kits for labeling DNA (e.g., open chromatin-associated gDNA). The method can comprise contacting double-stranded DNA (dsDNA), such as gDNA, with a transposome to generate a plurality of dsDNA fragments each comprising a first 5? overhang and a second 5? overhang. The transposome can comprise a transposase, a first adaptor having a first 5? overhang, and a second adaptor having a second 5? overhang. The first 5? overhang can comprise a complement of a target-binding region of a bead oligonucleotide. The first 5? overhang can comprise a coupling sequence. The second 5? overhang can comprise a universal sequence. There are provided, in some embodiments, coupling oligonucleotides comprising a 5? complement of the coupling sequence and a 3? complement of a target-binding region of a bead oligonucleotide.

Abstract: Disclosed herein include systems, methods, compositions, and kits for performing targeted single cell mRNA sequencing assays. Capture oligonucleotides capable of specifically binding to target nucleic acid species are provided in some embodiments. Depletion oligonucleotides capable of specifically binding to undesirable nucleic acid species are provided in some embodiments. The method can comprise random priming and extension of barcoded transcripts followed by one or more enrichment and/or depletion steps using said capture oligonucleotides and/or depletion oligonucleotides. Immune repertoire profiling methods are also provided in some embodiments.

Abstract: Disclosed herein include systems, methods, compositions, and kits for labeling nucleic acid targets in a sample. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3? end and are subsequently barcoded on the 5? end following a template switching reaction and intermolecular and/or intramolecular hybridization and extension. 5?- and/or 3?-barcoded nucleic acid targets can serve as templates for amplification reactions and/or random priming and extension reactions to generate a sequencing library. The method can comprise generating a full-length sequence of the nucleic acid target by aligning a plurality of sequencing reads. Immune repertoire profiling methods are also provided in some embodiments.

Abstract: Disclosed herein include systems, methods, compositions, and kits for quantitative analysis of a plurality of cellular component targets of cells of interest. In some embodiments, an oligonucleotide associated with a cellular component-binding reagent (e.g., an antibody) is associated with one or more detectable moieties (e.g., luminescent moieties, fluorescent moieties, a phosphorescent moieties). In some embodiments, the presence of the detectable moiety in the binding reagent oligonucleotide enables the cellular component-binding reagent to be employed for both fluorescence analysis (e.g., cell sorting) and sequence analysis (e.g., protein expression profiling).

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a carbohydrate binding reagent or a cell membrane permeable reagent associated with an oligonucleotide, such as a sample indexing oligonucleotide. Different oligonucleotides can have different sequences. Sample origin of cells can be determined based on the sequences of the oligonucleotides by, for example, barcoding the oligonucleotides.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification and protein expression profiling. A sample indexing composition, or a composition for protein expression profiling, can comprise, for example, a protein binding aptamer associated with an oligonucleotide, such as a sample indexing oligonucleotide. Different oligonucleotides can have different sequences. Sample origin of cells, or protein expression profiles of cells, can be determined based on the sequences of the oligonucleotides by, for example, barcoding the oligonucleotides.