Provided herein are methods for enrichment of nucleic acid libraries for non-artefactual on-target molecules that produce bona fide sequencing reads while eliminating or reducing artefactual on-target molecules that produce wasted reads thereby improving sequencing efficiency. Methods comprise the neutralization of a single artefactual strand of a dsDNA molecule and capture of the non-artefactual strand thereby generating enriched sequencing libraries.

Provided herein are methods for enrichment of nucleic acid libraries for non-artefactual on-target molecules that produce bona fide sequencing reads while eliminating or reducing artefactual on-target molecules that produce wasted reads thereby improving sequencing efficiency. Methods comprise the neutralization of a single artefactual strand of a dsDNA molecule and capture of the non-artefactual strand thereby generating enriched sequencing libraries.

Recombinant transposon end nucleic acids are described that can incorporate barcodes, sequencing primers, or other functional biological sequences. This application also describes mixtures and uses of the recombinant transposon end nucleic acids.

Recombinant transposon end nucleic acids are described that can incorporate barcodes, sequencing primers, or other functional biological sequences. This application also describes mixtures and uses of the recombinant transposon end nucleic acids.

Disclosed herein are methods of identifying or engineering a polynucleotide sequence for directing tissue-specific gene expression. The methods may further include creating a regulatory element fragment library. Further disclosed are vectors comprising a tissue-specific regulatory element identified by the methods.

Disclosed are compositions and methods relating to sequence-controlled storage objected. The disclosed sequence-controlled storage objects can include (a) one or more different sequence-controlled polymers, and (b) a plurality of different feature tags. The sequence-controlled storage object can include (a) one or more different sequence-controlled polymers, and (b) a plurality of different digit tags. Also disclosed are methods of storing desired sequence-controlled polymers as a sequence-controlled storage object, comprising assembling a sequence-controlled storage object from (i) one or more different sequence-controlled polymers, (ii) a plurality of different feature tags, and (iii) optionally one or more encapsulating agents. Also disclosed are methods of automating the assembly of a sequence-controlled storage object comprising using a device with flow.

The present disclosure provides methods and compositions for molecular tagging of complex populations of nucleic acid molecules. The disclosure provides methods and compositions to obtain phase information of tagged nucleic acid molecules from high-throughput nucleic acid sequencing data.

Described herein are methods for making genetically modified cells by introducing combinations of genetic variants (designed or random) or constructs (genes or otherwise arbitrary DNA) into a population of cells, and for tracking each variant combination by sequentially building an array of barcodes at a common locus (chromosomal or plasmid), termed the barcode locus. Also described are the cells made by such methods.

Described herein are methods for making genetically modified cells by introducing combinations of genetic variants (designed or random) or constructs (genes or otherwise arbitrary DNA) into a population of cells, and for tracking each variant combination by sequentially building an array of barcodes at a common locus (chromosomal or plasmid), termed the barcode locus. Also described are the cells made by such methods.

The present invention provides compositions, systems, kits, and methods for analyzing the interaction of T-cells and neoantigen presenting cells (and other cells) via discrete entity (e.g., droplet) microfluids. In certain embodiments, a microfluidic device is used to merge a discrete entity containing a T-cell, and a discrete entity containing a neoantigen presenting cell, at a merger region via a trapping element in order to generate a combined discrete entity. In particular embodiments, at least one thousand of such combined discrete entities are formed in about one second. In some embodiments, whether the receptor on the T-cell sufficiently binds the neoantigen to activate the T-Cell is detected (e.g., via detection of cytokine or granzyme B release). In certain embodiments, provided herein are methods for identifying polyfunctional T-cells or NK-cells, as well as methods of screening for such cells that would be cytotoxic if injected into a subject.