The present invention provides methods and systems for encoding and decoding of synthesis steps and conditions of combinatorial synthesis of molecular library on carrier-beads. The encoding is performed at each step of synthesis by attachment of smaller fluorescently labelled beads (label-beads) to the surface of a carrier-bead (carrier-bead). The number of label-beads should be such that each is spatially resolvable on a surface of the carrier-bead. Alternatively label-beads are detachable, or the carrier-bead are dissolvable, so the label-beads could be dispersed over large enough distance to be resolved spatially. The fluorescent spectrum of each of the label-beads carries information of the synthesis step and synthesis, i.e., a spectral barcode or binary encoding system. During decoding of the spectrally identified label-beads, a fluorescent spectrum of each spatially resolvable label-bead is determined.

Methods, compositions, and systems for distributing nucleic acids into array regions are provided. The methods, compositions, and systems utilize nucleic acid condensing agents to increase efficiency of distribution of the nucleic acids into the array regions. Various methods for facilitating distribution of the nucleic acids to the array regions are provided.

Inventions covered include methods, systems, and compositions for sample processing, involving morphology-adjustable (e.g., tunable on-demand) functionalized particles. In some embodiments, a method can include distributing a set of functionalized particles, in a first morphological state, across a set of partitions; transitioning the set of functionalized particles, at the set of partitions, from the first morphological state to a second morphological state; transitioning the set of functionalized particles, at the set of partitions, from the second morphological state to a third morphological state, and inducing interactions between the set of functionalized particles and a set of targets, within the set of partitions and according to a set of operations with a set of process fluids.

Analyte filter arrays and methods for making an analyte filter array are provided. The arrays are formed using a dispersion of filter particles having selected moieties attached to the surface of the particles and a microarray having complementary moieties formed in an array on a substrate, such that each filter particle is attached to a selected region of the microarray. The moiety on the substrate may be RNA or DNA or other molecule. The substrate may be a surface of a detector array, a membrane that may be placed in registration with the detector array or a stamp used to transfer the filter array to a detector array.

Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include features and materials that are provided on or in the support of a patterned array and that return at least a portion of incident light by reflection. The fiducial markers may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the patterned array.

The invention relates to a method for analyzing molecular properties and/or reaction conditions, comprising a step of providing a first store having a first surface, wherein a specific selection of sample molecules is directly or indirectly bonded to the surface in a defined arrangement, a step of producing at least two transfer stores, wherein at least two additional surfaces are provided, and a reaction step, selected from the group comprising a transfer reaction, an amplification reaction, and/or a derivatization reaction, whereby product molecules can arise and said product molecules and/or the sample molecules bond to the surfaces, wherein there is a clear spatial association between the sample molecules of the first store and the product molecules and/or sample molecules of the transfer stores and the first store, the transfer stores, the sample molecules, the product molecules, the transfer reaction, the amplification reaction, and/or the derivatization reaction is analyzed.

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.

An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.

A method of depositing single particles onto a target comprises the steps of loading a particle suspension to a droplet dispenser having a suspension reservoir and a nozzle section, detecting particles in the nozzle section, testing a single particle condition of the droplet dispenser, wherein it is determined whether an ejection region of the nozzle section includes one single particle, and operating the droplet dispenser for dispensing a droplet, wherein the droplet is dispensed onto the target, if the single particle condition is fulfilled, or the droplet is dispensed into a collection reservoir, if the single particle condition is not fulfilled, wherein the step of testing the single particle condition further includes determining whether a sedimentation region adjacent to the ejection region is free of particles. Furthermore, a dispenser apparatus dispensing single particles onto a target is described.

Fiducial markers are provided on a patterned array of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations and layouts that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include non-rectilinear layouts that may provide for more robust location of both the fiducial markers and sites of the patterned array.