Abstract: Disclosed herein include systems, methods, compositions, and kits for full-length whole transcriptome analysis (WTA). Some embodiments comprise 5?-based, 3?-based, and internal-based gene expression profiling. Immune repertoire profiling methods are also provided in some embodiments.

Abstract: Disclosed herein include systems, methods, compositions, and kits for reducing non-specific noise-causing oligonucleotides in library preparations. Capture particles present in PCR reactions that are derived from partitions that did not contain a cell (e.g., noise capture particles) provide a significant source of non-specific nucleic acid and noise in single cell multiomics library preparations. In some embodiments of the methods provided herein, said noise capture particles are removed by a variety of approaches.

Abstract: Disclosed herein include systems, methods, compositions, and kits for associating single cell sequencing data with imaging data (e.g., phenotypic data). In some embodiments, particle indexing oligonucleotides are associated with reference particles. Reference particles can comprise one or more detectable moieties. The particle indexing oligonucleotide can comprise a particle type identifier (PTI) and a unique particle identifier (UPI). The PTI and the UPI can be employed to identify of the imaged partition from which a sequenced nucleic acid target molecule originated.

Abstract: Disclosed herein include systems, methods, compositions, and kits for determining the spatial location and copy number of targets (e.g., nucleic acid targets, cellular component targets) in a sample. There are provided, in some embodiments, substrates comprising a plurality of spatial regions. A plurality of oligonucleotide barcodes can be associated with each of the spatial regions and can comprise a predetermined spatial label. Oligonucleotide barcodes of the same spatial region can comprise the same spatial label, and oligonucleotide barcodes of the different spatial regions can comprise different spatial labels. The method can comprise contacting the substrate with a sample such that each distinct spatial region contacts a distinct spatial location of the sample. The method can comprise in situ extension (e.g., reverse transcription) of the oligonucleotide barcodes.

Abstract: Disclosed herein include systems, methods, compositions, and kits for full-length whole transcriptome analysis (WTA). Some embodiments comprise 5?-based, 3?-based, and internal-based gene expression profiling. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3? end with the first plurality of oligonucleotide barcodes and subsequently barcoded on the 5? end following a template switching reaction and intermolecular hybridization with a second plurality of oligonucleotide barcodes and extension. In some embodiments, extended barcoded nucleic acid molecules are contacted with a transposome and tagmentation products are barcoded with a third plurality of oligonucleotide barcodes. Immune repertoire profiling methods are also provided in some embodiments.

Abstract: Antibodies attached to oligonucleotides can bind to proteins of cells. These oligonucleotides can be released and captured by solid support oligonucleotides attached to solid supports. A detection oligonucleotide can hybridize to the captured oligonucleotides forming a sandwich of solid support oligonucleotide-captured oligonucleotide-detection oligonucleotide. The detection oligonucleotide and the captured oligonucleotides it binds to can be quantified by, for example, the fluorescent intensity of second detectable moieties (e.g., dye(s)) on the detection oligonucleotide. The identity of the protein quantified can be determined by, for example, the fluorescent intensity of first detectable moieties (e.g., dye(s)) on the solid support with the sandwich of solid support oligonucleotide-captured oligonucleotide-detection 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 preserving and/or recovering RNA from fixed and/or permeabilized cells, for example for single cell analysis. In some embodiments, the fixed and/or permeabilized cells are for measuring intracellular target (e.g., protein) expression.

Abstract: Disclosed herein include systems, methods, kits, and compositions for labeling nuclear target-associated DNA in a cell. Some embodiments provide digestion compositions comprising a DNA digestion enzyme and a binding reagent capable of specifically binding to the nuclear target. Some embodiments provide conjugates comprising a transposome and a binding reagent capable of specifically binding to a nuclear target. The transposome can comprise a transposase (e.g., Tn5 transposase), a first adaptor having a first 5? overhang, and a second adaptor having a second 5? overhang. The methods can comprise contacting a permeabilized cell comprising a nuclear target associated with dsDNA, such as genomic DNA (gDNA), with the compositions provided herein to generate a plurality of nuclear target-associated dsDNA fragments (e.g., nuclear target-associated gDNA fragments) each comprising the one or two single-stranded overhangs.

Abstract: Disclosed herein include systems, methods, compositions, and kits for using decoy polynucleotides in noise reduction. Decoy oligonucleotides provided herein can, in some embodiments, prevent or reduce undesirable non-specific binding of intracellular target-binding reagent specific oligonucleotides or protein target-binding reagent specific oligonucleotides to non-target cellular/endogenous nucleic acids, and therefore reduce noise in methods provided herein, such as, for example, single cell multiomics analysis.

Abstract: Disclosed herein include systems, methods, kits, and compositions for labeling nuclear target-associated DNA in a cell. Some embodiments provide digestion compositions comprising a DNA digestion enzyme and a binding reagent capable of specifically binding to the nuclear target. Some embodiments provide conjugates comprising a transposome and a binding reagent capable of specifically binding to a nuclear target. The transposome can comprise a transposase (e.g., Tn5 transposase), a first adaptor having a first 5? overhang, and a second adaptor having a second 5? overhang. The methods can comprise contacting a permeabilized cell comprising a nuclear target associated with dsDNA, such as genomic DNA (gDNA), with the compositions provided herein to generate a plurality of nuclear target-associated dsDNA fragments (e.g., nuclear target-associated gDNA fragments) each comprising the one or two single-stranded overhangs.

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: Systems, methods, compositions, and kits for measuring secreted factors from cells are disclosed herein, including those capable of determining single cell secretion activity and protein expression and/or gene expression simultaneously. Disclosed herein include solid supports comprising a plurality of capture probes capable of specifically binding to at least one of the plurality of secreted factors secreted by a single cell. Also disclosed herein include secreted factor-binding reagents capable of specifically binding to a secreted factor bound by a capture probe. A secreted factor-binding reagent can comprise a secreted factor-binding reagent specific oligonucleotide comprising a unique factor identifier sequence for the secreted factor-binding reagent.

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 determining the presence of a single cell mRNA sequencing assay workflow failure, including determining a failure in barcoding copies of a nucleic acid target and determining a failure in sequencing library generation. There are also provided, in some embodiments, compositions, methods, and systems for determining the sequencing status of sequencing library members (e.g., saturated sequencing or under sequencing). Compositions comprising a predetermined copy number of barcoded control nucleic acids are also provided herein.

Abstract: Disclosed herein include systems, methods, compositions, and kits for performing intracellular AbSeq assays. There are provided, in some embodiments, methods for measuring intracellular target expression. The method can comprise fixing and permeabilizing a plurality of cells before contacting with a plurality of intracellular target-binding reagents capable of specifically binding to an intracellular target. Intracellular target-binding reagents can comprise an intracellular target-binding reagent specific oligonucleotide comprising a unique intracellular target identifier for the intracellular target-binding reagent specific oligonucleotide. The method can further comprise removing the permeabilizing agent and reversing the fixation.

Abstract: Disclosed herein include systems, methods, kits, and compositions for labeling nuclear target-associated DNA in a cell. Some embodiments provide digestion compositions comprising a DNA digestion enzyme and a binding reagent capable of specifically binding to the nuclear target. Some embodiments provide conjugates comprising a transposome and a binding reagent capable of specifically binding to a nuclear target. The transposome can comprise a transposase (e.g., Tn5 transposase), a first adaptor having a first 5? overhang, and a second adaptor having a second 5? overhang. The methods can comprise contacting a permeabilized cell comprising a nuclear target associated with dsDNA, such as genomic DNA (gDNA), with the compositions provided herein to generate a plurality of nuclear target-associated dsDNA fragments (e.g., nuclear target-associated gDNA fragments) each comprising the one or two single-stranded overhangs.

Abstract: Provided are a system and method for managing application programs for terminals. The system for managing application programs for terminals is configured to manage application programs of given terminals through an application synchronization function all at once. It is possible to install, delete, or change the dedicated application programs of the terminals all at once and purchase the application programs through a designated market, independently of whether the terminals have different platforms, to receive and apply installation information.

Abstract: An application program management method and apparatus using information are provided. The application program management method includes: in response to the state of an application program being changed in a first terminal, notifying a second terminal of the occurrence of an application program update in the first terminal; and in response to the second terminal recognizing the occurrence of an application program update in the first terminal, providing the second terminal with the state-changed application program or updated information relating to the state-changed application program.