Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.

Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.

The present invention relates to a method of identifying a target genomic nucleic acid sequence including hybridizing a set of probes to the target genomic nucleic acid sequence, wherein the set of probes has a unique associated barcode sequence for identification of the target genomic nucleic acid sequence, wherein each probe of the set includes (1) a complementary sequence complementary to a first strand of the target genomic nucleic acid sequence and (2) the associated barcode sequence or a portion of the associated barcode sequence, sequencing the associated barcode sequence from probes hybridized to the target genomic nucleic acid sequence using a fluorescence-based sequencing method, and identifying the target genomic nucleic acid sequence by the sequenced barcode sequence.

The present invention relates to a method of identifying a target genomic nucleic acid sequence including hybridizing a set of probes to the target genomic nucleic acid sequence, wherein the set of probes has a unique associated barcode sequence for identification of the target genomic nucleic acid sequence, wherein each probe of the set includes (1) a complementary sequence complementary to a first strand of the target genomic nucleic acid sequence and (2) the associated barcode sequence or a portion of the associated barcode sequence, sequencing the associated barcode sequence from probes hybridized to the target genomic nucleic acid sequence using a fluorescence-based sequencing method, and identifying the target genomic nucleic acid sequence by the sequenced barcode sequence.

The present disclosure generally relates to spatial detection of a nucleic acid, such as a genomic DNA or a RNA transcript, in a cell comprised in a tissue sample. The present disclosure provides methods for detecting and/or analyzing nucleic acids, such as chromatin or RNA transcripts, so as to obtain spatial information about the localization, distribution or expression of genes in a tissue sample. The present disclosure thus provides a process for performing “spatial transcriptomics” or “spatial genomics,” which enables the user to determine simultaneously the expression pattern, or the location/distribution pattern of the genes expressed or genes or genomic loci present in a single cell while retaining information related to the spatial location of the cell within the tissue architecture.

The present disclosure generally relates to spatial detection of a nucleic acid, such as a genomic DNA or a RNA transcript, in a cell comprised in a tissue sample. The present disclosure provides methods for detecting and/or analyzing nucleic acids, such as chromatin or RNA transcripts, so as to obtain spatial information about the localization, distribution or expression of genes in a tissue sample. The present disclosure thus provides a process for performing “spatial transcriptomics” or “spatial genomics,” which enables the user to determine simultaneously the expression pattern, or the location/distribution pattern of the genes expressed or genes or genomic loci present in a single cell while retaining information related to the spatial location of the cell within the tissue architecture.

Provided herein are compositions and methods for simultaneously measuring target oligonucleotides and protein in single cells. Compositions comprise an antibody-tagged oligonucleotide, including an origin specific barcode handle sequence, a first primer handle sequence, a second primer handle sequence, and a target binding region. The composition may also include an adapter sequence, a unique molecular identifier (UMI), and a poly-A sequence. Methods for simultaneously measuring target oligonucleotides and protein in single cells generally involve delivering a mixture of the composition to a population of cells and encapsulating individual cells in an individual discrete volume comprising PCR primers on a bead. The individual discrete volume may be suspended in a reverse transcription mixture and the nucleotide sequence of the origin specific barcode handle sequence may be detected, thereby assigning the target oligonucleotide and protein of interest to a specific individual discrete volume, while maintaining information about sample origin of the target oligonucleotide.

Provided herein are compositions and methods for simultaneously measuring target oligonucleotides and protein in single cells. Compositions comprise an antibody-tagged oligonucleotide, including an origin specific barcode handle sequence, a first primer handle sequence, a second primer handle sequence, and a target binding region. The composition may also include an adapter sequence, a unique molecular identifier (UMI), and a poly-A sequence. Methods for simultaneously measuring target oligonucleotides and protein in single cells generally involve delivering a mixture of the composition to a population of cells and encapsulating individual cells in an individual discrete volume comprising PCR primers on a bead. The individual discrete volume may be suspended in a reverse transcription mixture and the nucleotide sequence of the origin specific barcode handle sequence may be detected, thereby assigning the target oligonucleotide and protein of interest to a specific individual discrete volume, while maintaining information about sample origin of the target oligonucleotide.

The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.