A sample carrier for assaying can include a plurality of pins having a surface that is capable of picking up at least one substance on the surface. The pins can be arranged such that one or more of the plurality of pins are introduced into a corresponding reaction vessel of a microplate. The sample carrier can be divided into a plurality of modules, with each of the plurality of modules comprising one or more pins of the plurality of pins. Methods of use include placing the sample carrier onto a microplate so that at least the one or more of the plurality of pins extend into the corresponding reaction vessel of the microplate.

Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate using a minimal mask scheme. Systems and kits employing the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photomasks and photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.

Provided herein, in some embodiments, are devices, systems and methods for high-throughput single-cell polyomics (e.g., genomic, epigenomic, proteomic and/or phenotypic profile) analyses.

Apparatuses, compositions and processes for DNA barcode deconvolution are described herein. A DNA barcode may be used to provide a bead specific identifier, which may be detected in situ using hybridization strategies. The DNA barcode provides identification by sequencing analysis. The dual mode of detection may be used in a wide variety of applications to link positional information with assay information including but not limited to genetic analysis. Methods are described for generation of barcoded single cell sequencing libraries. Isolation of nucleic acids from a single cell within a microfluidic environment can provide the foundation for cell specific sequencing library preparation.

Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate. Compositions such as nucleic acid arrays produced by the methods are also disclosed. Further provided in some aspects are methods for light-controlled in situ refinement of nucleic acid array feature boundaries. In some embodiments, a method disclosed herein comprises using photoresist for photocontrollable removal, blocking, and/or inactivation of nucleic acid molecules at feature boundaries. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, ligation, and further interceded and/or followed by one or more rounds of photocontrollable refinement of array feature boundaries, to improve spatial array resolution and sensitivity.

Provided herein are monoliths with attached recognition compounds which selectively bind ligands, methods of preparing such monoliths, arrays thereof and uses thereof. For example, monoliths provided herein can be used in columns and arrays thereof.

Complete nucleic acid library preparation devices are provided. Aspects of the devices include: a thermal chip module comprising multiple nodes; one or more plate locations; a robotically controlled liquid handler configured to transfer liquid between the one or more plate locations and the thermal chip module; and a bulk reagent dispenser configured to access each node of the thermal chip module.

Provided herein are monoliths with attached recognition compounds which selectively bind ligands, methods of preparing such monoliths, arrays thereof and uses thereof. For example, monoliths provide herein can be used in columns and arrays thereof.

This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Arrays and substrates comprising a material, in particular capture agents and/or detectable targets, attached to the substrates along substantially parallel lines forming a barcoded pattern and related methods and systems.