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.

A method of storing information using monomers such as nucleotides is provided including converting a format of information into a plurality of bit sequences of a bit stream with each having a corresponding bit barcode, converting the plurality of bit sequences to a plurality of corresponding oligonucleotide sequences using one bit per base encoding, synthesizing the plurality of corresponding oligonucleotide sequences on a substrate having a plurality of reaction locations, and storing the synthesized plurality of corresponding oligonucleotide sequences.

A sector marker for placement over a tubesheet and defining an opening for performing maintenance on an open tube located below the sector marker, the sector marker positioned over the tubesheet by at least two pins extending below the sector marker and respectively received in tube openings below the sector marker. A device and a method for easily and accurately marking and identifying the location of the tubes in a reactor vessel and for keeping track, in real-time, of the tasks performed on the tubes.

Provided in some aspects are methods for light-controlled in situ surface patterning of an array. Compositions such as nucleic acid arrays produced by the methods are also disclosed.

Disclosed herein are methods for tracking solutions, (e.g., reaction conditions in solutions). In some embodiments, the method comprises: contacting a first lanthanide-chelator complex to a first solution to generate a first barcoded solution, wherein the first lanthanide-chelator complex comprises a first lanthanide chelated by a first chelator; contacting a second lanthanide-chelator complex to a second solution to generate a second barcoded solution, wherein the second lanthanide-chelator complex comprises a second lanthanide chelated by a second chelator; mixing the first barcoded solution and the second barcoded solution to form one or more mixtures; and identifying the first lanthanide ions in the mass spectrum and the second lanthanide ions in the mass spectrum to track the condition of each of the one or more mixtures.

Disclosed herein are methods for producing high density cellular arrays. In some embodiments, the methods comprise: providing a sample comprising a plurality of cells; and introducing the plurality of cells in the sample into microwells of a microwell array to produce a cellular array, wherein the microwell array comprises 500 or more microwells per inch.sup.2, and wherein 25% or more of the microwells of the cellular array comprise a single cell. The disclosed methods can be used for producing a high density synthetic particle array and a high density reagent array.

The present disclosure relates to a microfluidic device and a method allowing the generating and screening of combinatorial samples. A microfluidic device for producing droplets of at least one sample into an immiscible phase is provided, the device comprising a droplet maker connecting an immiscible phase channel and a sample channel having at least one sample inlet connected to at least one sample inlet channel injecting the at least one sample into the sample channel, wherein the injection of the at least one sample is controlled by at least one sample valve, so that the at least one sample flows either towards a sample waste outlet or into the at least one sample inlet channel, wherein different sample inlet channel of the at least one sample inlet channel have the same hydrodynamic resistance resulting from the length, height and width of each sample inlet channel upstream of the droplet maker.

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.

Methods of generating a nucleic acid signature for identifying particles associated in a partition are provided. In one aspect, the method comprises: partitioning a sample into a plurality of partitions comprising a particle comprising a solid support surface, the solid support surface having a plurality of oligonucleotide primers conjugated thereon, wherein the oligonucleotide primers comprise a barcode sequence, and wherein the partitions have 0, 1, or more than 1 particles per partition; providing in a partition a substrate comprising a barcode sequence or repeating clonal barcode sequences; and in the partition, associating a first particle conjugated to oligonucleotide primers comprising a first barcode sequence and a second particle conjugated to oligonucleotide primers comprising a second barcode sequence to a barcode sequence from the substrate, thereby generating a nucleic acid signature for the particles in the partition.

A kit for use with a nucleic acid sequencing instrument can include a plurality of combinatorial barcodes sequences meeting the following criteria: each of the combinatorial barcode sequences comprise a plurality of iterations of a sequence motif, where the sequence motif comprises a first nucleotide base from a first group of nucleotide bases followed by a second nucleotide base from a second group of nucleotide bases, the first group and the second group differing from each other; and the plurality of combinatorial barcode sequences is at least 1,000,000 different barcode sequences.