Disclosed herein include methods, compositions, and systems for extending particle-associated oligonucleotides. In some embodiments, the methods of extending particle-associated oligonucleotides enable efficient methods of preparing a library of barcoded beads. It is also provided, in some embodiments, hydrogel beads degradable upon application of a chemical stimulus that comprise releasably attached oligonucleotides.

Devices and methods are provided for selectively expelling and/or transferring nucleic acids. In one aspect, the device includes a component (e.g., a piezoelectric or an acoustic component) configured to align with one or more features on a solid support, such that when in use, the component (e.g., the piezoelectric or acoustic component) generates a mechanical force to selectively expel and/or transfer one or more volumes of nucleic acid from the solid support. The solid support can include a plurality of discrete features, each feature having a volume (e.g., droplet) of nucleic acid thereon. A power source can be included to provide an electric current to the component (e.g., the piezoelectric or acoustic component, if present) to generate mechanical force. The device can be used for nucleic acid singulation during and/or after assembly.

Devices and methods are provided for selectively expelling and/or transferring nucleic acids. In one aspect, the device includes a component (e.g., a piezoelectric or an acoustic component) configured to align with one or more features on a solid support, such that when in use, the component (e.g., the piezoelectric or acoustic component) generates a mechanical force to selectively expel and/or transfer one or more volumes of nucleic acid from the solid support. The solid support can include a plurality of discrete features, each feature having a volume (e.g., droplet) of nucleic acid thereon. A power source can be included to provide an electric current to the component (e.g., the piezoelectric or acoustic component, if present) to generate mechanical force. The device can be used for nucleic acid singulation during and/or after assembly.

Provided are a vesicular adaptor and a single-chain cyclic library constructed by using the adaptor. The library can be used for RNA sequencing and other sequencing platforms dependent on a single-stranded cyclic library, and has the advantage of high throughput sequencing, high accuracy and simple operations.

Provided are a vesicular adaptor and a single-chain cyclic library constructed by using the adaptor. The library can be used for RNA sequencing and other sequencing platforms dependent on a single-stranded cyclic library, and has the advantage of high throughput sequencing, high accuracy and simple operations.

Described are methods for selecting an amount of a critical parameter (such as an amount of a sequencing library, amount of a capture probe library, or a number of amplification cycles) for direct targeted sequencing. The methods include hybridizing capture probes in a capture probe library to surface-bound oligonucleotides; extending the surface-bound oligonucleotides using the hybridized capture probes as a template; hybridizing nucleic acid molecules from a sequencing library to the surface-bound capture probes; extending the surface-bound capture probes using the hybridized nucleic acid molecules as a template; amplifying the surface-bound complements of the nucleic acid molecules by bridge amplification for a number of amplification cycles; sequencing the amplified surface-bound complements of the nucleic acid molecules to determine an average cluster density after a predetermined number of sequencing cycles; repeating these steps at a plurality of different amounts of the critical parameter; and selecting an amount of the critical parameter.

De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.

De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.

Disclosed are methods and systems for determining the three-dimensional structure of chromatin in eukaryotic cells. More specifically, disclosed are methods and systems for obtaining chromatin structural information by surface immobilization that includes tethering crosslinked protein:DNA complexes and/or ligated DNA complexes to media such as beads, gels, and or matrices during the conformation capture assay. In general, the method includes flash freezing a cell such that the structural organization of the chromatin or other protein:DNA complexes is preserved, cryomilling the cell, producing cross-linked protein:DNA complexes by cutting the chromatin using a chemical, physical or enzymatic method, substantially immobilizing the cross-linked protein:DNA complexes, ligating the cross-linked protein:DNA complexes intramolecularly such that the ligated protein:DNA complexes represent structural organization of the chromatin; characterizing the ligated DNA by sequencing or other methods; and identifying any structural organization of the chromatin. The structural organization preferably includes information relating to interacting loci of the chromatin.

The disclosure generally relates to systems, methods, and apparatuses for magnetic bead loading. An example embodiment of the disclosure relates to mixing magnetic beads with sequencing beads to form a solution. The solution containing both beads is injected onto a microchip having a plurality of microwells. The magnetic beads may have larger diameter than the microwell while the sequencing beads may have a smaller diameter, allowing them to enter and reside in the microwell. One or more magnets positioned under the microchip move back and forth across the microchip surface. The magnetic beads form a line and follow the movement of the magnets. During rounds of sweeping, the sequencing beads load into the respective wells. The magnets may be disengaged and the magnetic beads may be washed away after the sequencing beads are loaded.