Disclosed herein include methods, systems, compositions and kits for determining cell-cell interaction, for example, using nucleic acid sequencing. The method can match a cell barcode sequence associated with a cell of a plurality of cells with a cell barcode sequence associated with a partition of a plurality of partitions to identify the partition the cell has originated from in the plurality of partitions. In some embodiments, a pair of interacting cells within a partition are attached with a common cell barcode. The nucleic acid sequences of the pair of interacting cells having the common cell barcode can be tracked to the partition the pair of interacting cells has originated from, where phenotypic observables of the interacting cells can be obtained, for example, using optical imaging, thereby linking cell nucleic acid sequences such as expression profiles to cell functionality and the nature of the cell-cell interaction.

Disclosed herein include methods, systems, compositions and kits for determining cell-cell interaction, for example, using nucleic acid sequencing. The method can match a cell barcode sequence associated with a cell of a plurality of cells with a cell barcode sequence associated with a partition of a plurality of partitions to identify the partition the cell has originated from in the plurality of partitions. In some embodiments, a pair of interacting cells within a partition are attached with a common cell barcode. The nucleic acid sequences of the pair of interacting cells having the common cell barcode can be tracked to the partition the pair of interacting cells has originated from, where phenotypic observables of the interacting cells can be obtained, for example, using optical imaging, thereby linking cell nucleic acid sequences such as expression profiles to cell functionality and the nature of the cell-cell interaction.

Provided are methods and compositions for generating a deletion library, and methods and compositions for generating and identifying a defective interfering particle (DIP). Also provided are transposon cassettes. A subject method can include: inserting a transposon cassette comprising a target sequence for a sequence specific DNA endonuclease into a population of circular target DNAs to generate a population of transposon-inserted circular target DNAs; contacting the population of transposon-inserted circular target DNAs with the sequence specific DNA endonuclease to generate a population of cleaved linear target DNAs; contacting the population of cleaved linear target DNAs with one or more exonucleases to generate a population of deletion DNAs; and circularizing the deletion DNAs to generate a library of circularized deletion DNAs. The population of circular target DNAs can include viral genomic DNA. Also provided are human immunodeficiency virus (HIV) deletion mutants, e.g., interfering, conditionally replicating, HIV deletion mutants, and related constructs.

Disclosed herein include systems, methods, compositions, and kits for multiplexing single-cell RNA-sequencing (scRNA-seq) samples. In some embodiments, the methods comprise chemically tagging cells with identifying sample tags (e.g., barcoded DNA oligonucleotides).

Multiple polynucleotides with random sequences are collectively used as a molecular anti-counterfeiting tag. The polynucleotides are placed on an item as a molecular identifier of authenticity. Each position within the random sequences is synthesized using a predetermined ratio of nucleoside bases. With this technique the sequence of each polynucleotide is random but the ratio of nucleoside bases over the collection of synthetic polynucleotides is not. Verification of authenticity is achieved by sequencing a portion of the polynucleotides collected from the item and calculating the ratio of nucleoside bases at each position. If these ratios are the same or similar to the ratios used for synthesizing the polynucleotides, then the item is identified as authentic. The ratios of nucleoside bases and a description of the item may be stored in an electronic record that is used for validating authenticity of the item.

Multiple polynucleotides with random sequences are collectively used as a molecular anti-counterfeiting tag. The polynucleotides are placed on an item as a molecular identifier of authenticity. Each position within the random sequences is synthesized using a predetermined ratio of nucleoside bases. With this technique the sequence of each polynucleotide is random but the ratio of nucleoside bases over the collection of synthetic polynucleotides is not. Verification of authenticity is achieved by sequencing a portion of the polynucleotides collected from the item and calculating the ratio of nucleoside bases at each position. If these ratios are the same or similar to the ratios used for synthesizing the polynucleotides, then the item is identified as authentic. The ratios of nucleoside bases and a description of the item may be stored in an electronic record that is used for validating authenticity of the item.

Large numbers of polynucleotides with random sequences are used collectively as a molecular anti-counterfeiting tag. The polynucleotides are sequenced, placed on an item, and the sequences stored in an electronic record. Authenticity is determined by collecting the polynucleotides from a labeled item, sequencing those polynucleotides, and comparing the sequence to that stored in the electronic record. The number of polynucleotides used as the tag may be adjusted by aliquoting the original batch of randomly synthesized polynucleotides. Complexity of the polynucleotide tags may be increased by assembling individual polynucleotides from multiple dilutions to create longer assembled polynucleotides. Even if the sequences of the polynucleotides are known, the complexity of the tag can make the forgery of the tag itself technically difficult and prohibitively expensive.

Large numbers of polynucleotides with random sequences are used collectively as a molecular anti-counterfeiting tag. The polynucleotides are sequenced, placed on an item, and the sequences stored in an electronic record. Authenticity is determined by collecting the polynucleotides from a labeled item, sequencing those polynucleotides, and comparing the sequence to that stored in the electronic record. The number of polynucleotides used as the tag may be adjusted by aliquoting the original batch of randomly synthesized polynucleotides. Complexity of the polynucleotide tags may be increased by assembling individual polynucleotides from multiple dilutions to create longer assembled polynucleotides. Even if the sequences of the polynucleotides are known, the complexity of the tag can make the forgery of the tag itself technically difficult and prohibitively expensive.

Systems and methods are provided herein for encoding and storing information in nucleic acids. Encoded information is partitioned and stored in nucleic acids having native key-value pairs that allow for storage of metadata or other data objects. Computation on the encoded information is performed by chemical implementation of if-then-else operations. Numerical data is stored in nucleic acids by producing samples having nucleic acid sequences copy counts corresponding to the numerical data. Data objects of a dataset are encoded by partitioning of bytes into parts and encoding of parts along distinct libraries of nucleic acids. These libraries can be used as inputs for computation on the dataset.

Systems and methods are provided herein for encoding and storing information in nucleic acids. Encoded information is partitioned and stored in nucleic acids having native key-value pairs that allow for storage of metadata or other data objects. Computation on the encoded information is performed by chemical implementation of if-then-else operations. Numerical data is stored in nucleic acids by producing samples having nucleic acid sequences copy counts corresponding to the numerical data. Data objects of a dataset are encoded by partitioning of bytes into parts and encoding of parts along distinct libraries of nucleic acids. These libraries can be used as inputs for computation on the dataset.