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WO2024211324A1 - Unified detection workflow - Google Patents

Unified detection workflow Download PDF

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Publication number
WO2024211324A1
WO2024211324A1 PCT/US2024/022694 US2024022694W WO2024211324A1 WO 2024211324 A1 WO2024211324 A1 WO 2024211324A1 US 2024022694 W US2024022694 W US 2024022694W WO 2024211324 A1 WO2024211324 A1 WO 2024211324A1
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nucleic acid
analyte
circular
sample
array
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French (fr)
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Dajun Yuan
Pei Lin
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Videns Biosciences Inc
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Videns Biosciences Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/682—Signal amplification

Definitions

  • proteins may be assayed using primary and secondary antibody based approaches, while transcriptomes and genomes are assessed, and chromatin configuration assayed through distinct library preparation and sequencing approaches or through more disparate techniques.
  • transcriptomes and genomes are assessed, and chromatin configuration assayed through distinct library preparation and sequencing approaches or through more disparate techniques.
  • chromatin configuration assayed through distinct library preparation and sequencing approaches or through more disparate techniques.
  • SUMMARY Disclosed herein are compositions, systems and methods relating to accumulation of multi-level biological data through a single set of tools, techniques and outputs.
  • analytes such as proteins, RNA accumulation levels, DNA sequence, chromatin configuration, or other levels of information relevant to understanding, diagnosing or addressing a broad range of biological questions.
  • analytes such as proteins, RNA accumulation levels, DNA sequence, chromatin configuration, or other levels of information relevant to understanding, diagnosing or addressing a broad range of biological questions.
  • molecular mechanisms comprising analyte based probe circularization, followed by annealing of circularized probes to probe-binding primers on a solid particle such as a microbead so as to anchor the rolling circle amplification of the circularized probes.
  • the solid particles are Ref. No.
  • VDN.001WO deposited into positions such as wells on an array, at which they can be probed using sample specific, analyte type specific, analyte specific or other probes so as to identify the analyte corresponding to an RCA amplicon tethered to a bead at a particular position on the array.
  • Probes may be assayed using fluorescence detection, and detection may comprise single probe detection or multiple rounds of annealing by distinct probes so as to generate temporal fluorescence patterns corresponding to particular circularized probes or analytes that their circularization indicates.
  • Some embodiments relate to methods, such as methods for detecting an analyte or a plurality of analytes, of similar or difference chemical characteristics, said methods comprising one or more of the steps of generating a circular nucleic acid indicative of an analyte in a sample; annealing the circular nucleic acid to a surface oligo of a microparticle comprising a plurality of surface oligos; contacting the circular nucleic acid to a polymerase, dNTPs and a buffer consistent with nucleic acid extension; extending the surface oligo to form a concatemer of the circular nucleic acid tethered to the microparticle; depositing the microparticle in a well of a microarray; contacting the microarray to a first probe; and assaying for a signal indicative of the first probe bound to the concatemer.
  • generating the circular nucleic acid indicative of an analyte in a sample comprises annealing a linear precursor nucleic acid to a guide such that the 5’ end and 3’ end of the linear precursor are held in proximity, and ligating the 5’ and 3’ ends of the linear precursor.
  • the guide comprises a nucleic acid in the sample.
  • the guide comprises a nucleic acid that tags an antibody targeting an analyte in the sample.
  • the guide comprises a PCR amplicon from the sample. 6.
  • any previous embodiment such as embodiment 2, wherein the guide comprises an RNA molecule transcribed from a promoter- tagged fragment of the sample. 7.
  • the method of any previous embodiment, such as embodiment 2, wherein the guide is generated by tagmentation.
  • the method of any previous embodiment, such as embodiment 2, wherein the guide is generated by revers- transcription.
  • the method of any previous embodiment, such as embodiment 2, wherein the guide is generated by cleaving a nucleic acid of the sample.
  • the guide is generated by attaching primer binding sites at ends of a nucleic acid fragment of the sample. 11.
  • VDN.001WO previous embodiment such as embodiment 2, wherein the guide is generated by attaching transcription promoter sites ad at least one end of a nucleic acid fragment of the sample. 12. The method of any previous embodiment, such as embodiment 2, wherein the guide comprises an oligo tag attached to an analyte binding moiety. 13. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises an antibody binding domain. 14. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises an antibody. 15. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises a receptor. 16. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises a ligand.
  • any previous embodiment such as embodiment 1, wherein extending the surface oligo to form a concatemer of the circular nucleic acid tethered to the microparticle is performed under isothermal conditions.
  • the method of any previous embodiment, such as embodiment 23, wherein said isothermal conditions comprise room temperature extension.
  • the method of any previous embodiment, such as embodiment 23, wherein said isothermal conditions comprise extension at about 70 degrees C. 26.
  • the method of any previous embodiment, such as embodiment 1, wherein the microarray comprises at least 100 wells. 29.
  • the microarray comprises at least 1000 wells.
  • the microarray comprises at least 10,000 wells.
  • 31. The method of any previous embodiment, such as embodiment 1, wherein the microarray exhibits at least 90% well occupancy.
  • the method of any previous embodiment, such as embodiment 1, wherein the Ref. No. VDN.001WO microarray exhibits at least 95% well occupancy.
  • 33. The method of any previous embodiment, such as embodiment 1, wherein the microarray exhibits at least 99% well occupancy.
  • the method of any previous embodiment, such as embodiment 1, wherein assaying for a signal indicative of the first probe bound to the concatemer comprises capturing an image of the array. 35.
  • any previous embodiment, such as embodiment 34, wherein capturing the image comprises using a portable device.
  • 36. The method of any previous embodiment, such as embodiment 34, wherein capturing the image comprises using an optics system coupled to the array.
  • 37. The method of any previous embodiment, such as embodiment 1, comprising removing the first probe and contacting the microarray to a second probe, and assaying for a signal indicative of the second probe bound to the concatemer.
  • 38. The method of any previous embodiment, such as embodiment 1, wherein the method detects an analyte in the sample.
  • 39. The method of any previous embodiment, such as embodiment 1, wherein the method quantified an analyte in the sample. 40.
  • any previous embodiment, such as embodiment 1, wherein the method detects at least 100 distinct analytes in the sample. 41. The method of any previous embodiment, such as embodiment 1, wherein the method quantifies at least 100 distinct analytes in the sample. 42. The method of any previous embodiment, such as embodiment 1, wherein the method detects at least 1000 distinct analytes in the sample. 43. The method of any previous embodiment, such as embodiment 1, wherein the method quantifies at least 1000 distinct analytes in the sample. 44. The method of any previous embodiment, such as embodiment 1, wherein the method detects at least 10,000 distinct analytes in the sample. 45. The method of any previous embodiment, such as embodiment 1, wherein the method quantifies at least 10,000 distinct analytes in the sample. 46.
  • any previous embodiment such as embodiment 1, wherein the method is practiced on an individual at two distinct time points.
  • 47. The method of any previous embodiment, such as embodiment 46, wherein a treatment is administered to the patient between the two distinct time points.
  • 48. The method of any previous embodiment, such as embodiment 46, wherein a treatment is administered to the patient prior to the two distinct time points.
  • 49. The method of any previous embodiment, such as embodiment 46, wherein a treatment is administered to the patient concurrently with at least one of the two distinct time points.
  • a system comprising components for execution of the method of any previous embodiment, such as embodiment 1.
  • 51. The system of any previous embodiment, such as embodiment 50, configured to analyze a plurality of analytes. 52.
  • the composition of any previous embodiment, such as embodiment 57, wherein the well is a constituent of a patterned array of at least 10,000 wells.
  • 65. The composition of any previous embodiment, such as embodiment 56, further comprising a second microparticle bound to a second circular nucleic acid. 66.
  • the nucleic acid has a sequence corresponding to an expressed RNA molecule.
  • the composition of any previous embodiment, such as embodiment 67, wherein the nucleic acid has a sequence corresponding to an exposed chromosomal segment of chromatin. 70.
  • the first circular nucleic acid comprises a sample barcode.
  • the composition of any previous embodiment, such as embodiment 56, wherein the first circular nucleic acid comprises a segment indicative of a target analyte. 79.
  • a microparticle comprising a plurality of covalently bound surface oligos, at least one of which shares a common phosphodiester backbone with a concatemeric repeat of a circular nucleic acid molecule.
  • microparticle of any previous embodiment, such as embodiment 82, wherein the microarray comprises at least 100 wells.
  • the microparticle of any previous embodiment, such as embodiment 82, wherein the microarray comprises at least 10,000 wells.
  • the microparticle of any previous embodiment, such as embodiment 82, wherein the microarray exhibits at least 95% well occupancy.
  • An array comprising a plurality of wells, at least some of the wells each harboring no more than one nanoparticle per well, wherein the nanoparticles comprise covalently surface bound oligos, and wherein at least a portion of the nanoparticles are bound to circular reporter nucleic acids.
  • the circular reporter nucleic acids comprise circular reporter nucleic acids corresponding to target nucleic acids.
  • any previous embodiment such as embodiment 95, wherein the circular reporter nucleic acids comprise circular reporter nucleic acids corresponding to tags indicative of target analytes.
  • the circular reporter nucleic acids comprise a first population of circular reporter nucleic acids corresponding to target analyte nucleic acids and a second population of circular reporter nucleic acids corresponding to target analyte polypeptides.
  • any previous embodiment such as embodiment 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least two samples. 101. The array of any previous embodiment, such as embodiment 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least 10 samples. 102. The array of any previous embodiment, such as embodiment 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least 100 samples. 103. The array of any previous embodiment, such as embodiment 95, wherein the circular reporter nucleic acids comprise sample barcodes. 104.
  • any previous embodiment such as embodiment 97, wherein the circular reporter nucleic acids comprises target analyte identifying barcodes.
  • 105 The array of any previous embodiment, such as embodiment 98, wherein the circular reporter nucleic acids comprises target analyte identifying barcodes.
  • 106 The array of any one of any previous embodiment, such as embodiments 95 - 105, wherein the circular reporter nucleic acids are tethered to the at least a portion of the nanoparticles through the surface bound oligos.
  • 107 The array of any one of any previous embodiment, such as embodiments 95 - 105, wherein at least some of the surface oligos are extended to comprise concatemeric repeats of circular reporter nucleic Ref. No.
  • 110. The array of any previous embodiment, such as embodiment 95, wherein at least some of the plurality of wells are occupied.
  • the dataset comprises analyte data for at least 100 analytes.
  • the dataset comprises analyte data for at least 200 analytes.
  • the dataset is generated in no more than 4 hours. 118.
  • Fig. 1 depicts a workflow for chromatin access determination.
  • Fig. 2 depicts beads on an unpatterned surface.
  • Fig. 3 depicts a patterned surface of unloaded wells.
  • Fig. 4 depicts a patterned surface of wells into which beads have been loaded.
  • compositions systems and methods for concurrent, single mechanism monitoring of multiple types of analytes or cell state measurement such as Ref. No. VDN.001WO chromatin configuration measurements.
  • analytes or cell state measurement such as Ref. No. VDN.001WO chromatin configuration measurements.
  • the data may relate to presence or absence of one or more analytes, and may also comprise quantitative measurements of analyte abundance in a sample,
  • a large plurality of analytes or sets of analytes from common or distinct samples, such as samples subjected to distinct treatments or from individuals exhibiting distinct phenotypes, may be assayed concurrently on a single array, so as to facilitate concurrent, high throughput analysis of a broad range of analytes, analyte types and samples.
  • a mechanism common to a broad range of analyte detection approaches is the circularization of a linear analyte specific probe as a first step or early step in analyte detection.
  • Linear probes consistent with the disclosure herein comprise 5’ and 3’ end regions that are often selected to anneal to adjacent portions of a common guide or target.
  • Linear probes in some cases further comprise a region that is common to a particular sample and that distinguishes linear probes applied to that sample from linear probes applied to at least one other sample. This region is in some cases a sample barcode, or sample barcode region, or sample probe binding region, as it may be assayed for by binding to a labeled oligo probe.
  • Linear probes in some cases further comprise a region that is common to a particular organism or individual and that distinguishes linear probes applied to that organism or individual from linear probes applied to at least one other organism or individual.
  • Linear probes in some cases comprise a region that is common to a particular target analyte and that distinguishes linear probes applied to that target analyte from linear probes applied to at least one other target analyte.
  • This region is in some cases a target analyte barcode, or target analyte barcode region, or target analyte probe binding region, as it may be assayed for by binding to a labeled oligo probe.
  • this region is the 5’ end region, 3’ end region or a ligation product spanning the 5’ end region and 3’ end region that are often selected to anneal to adjacent portions of a common guide or target.
  • linear probes may comprise a distinct region that is common to a particular target.
  • Linear probes in some cases further comprise a random region, such as a random hexamer, heptamer, octamer, or of length such as 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater than 20 bases, that may serve as an individual linear probe identifier and that may be used in distinguishing a signal from one linear probe indicative of an analyte from a second linear probe indicative of the same analyte, such that the number of linear probes that identified a category of analyte in a sample can be quantified.
  • a random region such as a random hexamer, heptamer, octamer, or of length such as 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater than 20 bases, that may serve as an individual linear probe identifier and that may be used in distinguishing a signal from one linear probe indicative of an analyte from a second linear probe indicative of the same analyte,
  • Linear probes in some cases comprise a region that is universal or common to a plurality of linear probes, up to all linear probes used in an experiment. This region in some cases exhibits a distinct such as a higher GC concentration or melting point when annealed to reverse complement relative to a second region or the remainder of the linear probe.
  • Linear probes are often single stranded at their 5’ end regions and 3’ end regions. The probes may be single stranded throughout their length or may be double stranded at regions distal from the 5’ end regions and 3’ end regions.
  • Linear probes are in some cases selected to minimize off-target annealing, for example by selecting an overall GC bias that differs from that of nucleic acids in a target sample.
  • linear nucleic acids have a GC content of at least or at most 20%, 30%, 40%, 50%, 60%, 70%, or 80%, or a number spanned by or outside of that range.
  • the target is in some cases a complementary (or, more strictly speaking, reverse complementary) nucleic acid analyte target or amplification product therefrom. That is, nucleic acid targets such as DNA or RNA may serve as their own guides for detection by circular probes.
  • a nucleic acid analyte is subjected to amplification such that the amplification product may serve as a guide for the linear nucleic acid probe. That is, some nucleic acid analytes may be modified to add primer binding sites or RNA polymerase promoter sites at their end or ends so as to facilitate target nucleic acid analyte amplification, such that the amplification product (be it PCR product, transcript, reverse transcribed transcript or other analyte templated amplification product) serves as a guide for positioning of the linear nucleic acid probe 5’ and 3’ ends in proximity.
  • the guide or guide template is an oligo tag attached to a non-nucleic acid detection moiety such as an antibody, receptor, ligand, or other protein or other analyte binding partner.
  • a non-nucleic acid detection moiety such as an antibody, receptor, ligand, or other protein or other analyte binding partner.
  • the relation between the analyte and the guide sequence is arbitrary, but so long as the user knows which analyte corresponds to a given Ref. No. VDN.001WO barcode, its effect on downstream analysis is effectively identical to use of a single nucleic acid analyte as load.
  • raw samples are analyzed, as may be the case when an extracellular analyte is targeted, such as circulating free DNA or RNA, or a circulating pathogen or extracellular viral load, for example.
  • samples may be processed so as to make cytoplasmic, organellar or nuclear contents available for analysis. Processing may comprise cell lysis to access cytoplasmic contents such as cytoplasmic proteins, organelles or transcriptomes.
  • the nucleus is retained intact so as to protect chromatin structure or to exclude partially processed RNA from a transcriptome population.
  • the nuclear contents may be accessed by lysing or permeabilizing the nucleus of a eukaryotic sample.
  • samples may be processed to isolate or enrich for intact chromatin, nuclei, mitochondria, or other cellular structures.
  • Lipids may be assayed for accumulation or modification status, proteins may be assayed for accumulation levels, modification status such as phosphorylation status, or activity on a substrate.
  • Samples may be subjected to a broad range of processing steps prior to assaying.
  • Nucleic acids may be modified to facilitate polymerase chain reaction amplification, for example by adding one or more primer binding sites. Alternately or in combination, sample nucleic acids can be modified by the addition of a promoter so as to drive transcription of a target region.
  • Samples may be denatured, reverse transcribed, fixed, homogenized, phosphatase treated, tagmented, or subjected to any of a number of preparation approaches that are suitable for the analyte being assayed, without losing the ability to subject them to a common downstream analysis workflow.
  • localization of the linear nucleic acid probe 5’ and 3’ ends by the guide facilitates circularization of the linear analyte probe. Circularization is often effected by addition of a ligase and suitable buffer to a sample in which a guide and a linear nucleic acid probe are found or could potentially be found.
  • the circularized analyte probe is the common currency of many of the approaches herein. That is, circularization, be it through analyte binding to a guide tagged probe or through association with a natural or arbitrarily assigned guide or amplification product, is a first step in detection of any number among a broad range of analytes. Ref. No. VDN.001WO Furthermore, it facilitates the common downstream analysis workflow that allows common analysis of a broad range of disparate analytes. [0030] Independent of the analytes being assayed, one may adopt a common set of post- ligation processing steps in analyte analysis.
  • Samples are in some cases processed to extract nucleic acids, DNA or circular DNA, or to degrade all but nucleic acids, DNA or circular DNA. That is, in some cases samples are processed to extract nucleic acids. Alternately or in combination, in some cases samples are treated with, for example, one or more of a protease, an RNase or a DNA exonuclease, so as to remove sample constituents other than circular DNA. Sample treatment may also comprise heat treatment for inactivation of ligase activity or denaturation of circularized analyte probes from their guides. [0032] Circularized analyte probes may then be analyzed, with their detection serving as a proxy for analyte presence or abundance.
  • Some detection approaches comprise binding circularized analyte probes to a solid anchor or solid anchors such as a microparticle or bead population.
  • Exemplary beads comprise silica, polymer, magnetic material, metal or metal oxide. Magnetic beads, in particular, facilitate or are conducive to physical manipulation. Beads range in size from less than 20 nm to 500 um in diameter or more, such as 10nm, 20nm, 50nm, 100nm, 200nm, 500nm, 1um, 2um, 5um, 10um, 20um, 50um, 100 um, 200um, 500um, any diameter spanned by or outside of the mentioned range.
  • circular analyte probes are contacted to an excess of beads, such that beads have no more than one circular nucleic acid attached per bead. In alternate cases, beads are provided at concentrations or amounts so as to promote high bead occupancy by circularized analyte probes.
  • Beads are processed to have a coating of one or more oligonucleotides, such as oligonucleotides that anneal to or are the reverse complement of the universal region of the circularized analyte probes. The oligos are configured to be bound to the beads at their 5’ ends, or such that their 3’ ends are exposed and available for priming of 5’ to 3’ DNA synthesis.
  • the circular analyte probes anneal to the oligonucleotides such that a circular analyte probe is tethered to a bead via the bead surface oligonucleotide.
  • beads are configured to anneal to or become bound to a single circularized analyte probe, while in alternate cases beads are configured to accommodate a plurality of circularized analyte probes.
  • the beads are contacted to DNA extension reagents such as DNA polymerase, dNTPs, and buffer conditions sufficient to support DNA polymerization.
  • DNA extension reagents such as DNA polymerase, dNTPs, and buffer conditions sufficient to support DNA polymerization.
  • the bead oligo 3’ ends are then used to prime rolling circle amplification of bound circularized analyte probes, such that a concatemer of the circularized analyte probe is linked by a common phosphodiester backbone to the primer, and through the primer to the bead surface.
  • Rolling circle amplification is performed through an incubation step of, for example, no more than or no less than 1, 2, 3, 4, 5, 10, 15, 30, 60 or more than 60 minutes.
  • the circular analyte probes are then separated and, in some cases, discarded, and the beads are retained for further processing.
  • the beads are then contacted to a surface, such as a surface having patterned wells.
  • the wells are in some cases configured so as to accommodate one bead per well.
  • the beads are allowed to settle into the wells, or may be drawn into the wells for example using magnetic attraction, and the structure is in some cases washed to remove other reagents or unsettled beads.
  • Wells are selected to have a size to accommodate no more than one bead at a time.
  • Exemplary wells are about 10% larger than the bead they are configured to harbor. In some embodiments, using for example a 1um pitch, one observes more than 1 million wells per square millimeter such that there are more than 100 million wells on a 10mmx10mm chip.
  • Beads are loaded onto the surface so as to achieve a high rate of occupancy. Various embodiments exhibit occupancy rates of at least 70%, 80%, 85%, 90%, 91%, 92% 93% or greater than 93%.
  • beads are allowed to pack onto an unpatterned surface.
  • primers are packaged into hydrogel beads that are printed onto a surface.
  • a number of approaches may be used to visualize the rolling circle concatemers tethered to beads arrayed on a surface as disclosed herein.
  • sequencing oligos and other sequencing reagents are delivered to the beads and sequencing reactions, such as sequencing by synthesis, sequencing by binding or other sequencing by extension approach is used to determine the sequence of various regions of the concatemers, such as the sample region, organism or individual region, target analyte region, and randomer region.
  • rolling circle concatemers are identified via probing, such as with fluorescently labeled or otherwise labeled probes. In some cases, the probes correspond completely with the regions on the rolling circle concatemers to be assayed. In Ref. No.
  • each region variant is assigned a distinct color for the fluorophore attached to the probe used to detect it, such that emission wavelength upon binding and excitation corresponds with the identity of the probed region.
  • probes span a subset of the region to which they are directed, such that multiple partially overlapping or nonoverlapping probes may be used to probe a single region.
  • a particular region to be probed in combination with a subset of fluorophores tethered to probes temporally delivered to bind various subsections of the region, can specify a temporal pattern of fluorophore excitation that can specify the region without requiring a distinct fluorophore for each distinct region to be concurrently assayed.
  • multiple probes may be bound concurrently such that a color or wavelength combination is generated through the concurrent excitation of the probes’ attached fluorophores.
  • targets are iteratively probed using populations of probes that anneal to common target but that may differ from one another in their fluorophore label across rounds.
  • This dynamic range is accomplished independent of the analyte, such that proteins, metabolites, RNA, DNA, chromatin configuration or any other analyte to which a guide sequence can be assigned or attached may be assayed, comparably to other analytes, on a single surface.
  • a feature of the disclosure herein is that it can lead to rapid, high throughput analyte detection. Iterative probing and detection performed on a rolling circle concatemer population may comprise in some cases 5-10 detection cycles, depending on the number of samples or other factor, each cycle comprising probe hybridization (5min) and washing (1min), scanning (10min) and dehybridization (5min), for a cycle time of around 20 minutes. Various embodiments exhibit cycle times of, for example, no more than or no less than 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, or more than 30 minutes. [0053] Consistent with the disclosure herein are systems for practice of one or more of the steps above.
  • Such a system variously comprises distinct or common reservoirs for liner analyte probe populations, sample prep reagent such as cell or nucleus permeabilization reagents, tagmentation enzymes such as Tn5, amplification or transcription adapters, as well as DNA polymerase, RNA polymerase, guide tagged analyte binding moieties or other reagents suitable for particular analytes to be quantified, as well as ligase and ligation buffer.
  • sample prep reagent such as cell or nucleus permeabilization reagents
  • tagmentation enzymes such as Tn5, amplification or transcription adapters
  • DNA polymerase RNA polymerase
  • guide tagged analyte binding moieties or other reagents suitable for particular analytes to be quantified as well as ligase and ligation buffer.
  • Such systems may further comprise a heat block or other thermoregulatory functionality.
  • Beads may be delivered to the flow cell in which sample processing occurs.
  • circularized analyte probes may be extracted from a sample processing region Ref. No. VDN.001WO and delivered to a separate region for annealing to bead primers and rolling circle amplification to form concatemers on the bead surfaces.
  • This region may be distinct from or may be the array portion of the system. That is, beads may be decorated with rolling circle concatemer amplicons distinct from or in proximity to the array. In either case, the end result is that concatemer loaded beads are deposited into wells or onto an unpatterned surface of an array.
  • Deposited beads are probed so as to identify one or more of their sample of origin, organism or individual of origin, target analyte detected, and this information is correlated to array position to identify and in some cases quantify the analyte indicated by the circularized analyte probes.
  • Probing in some cases requires that the system has probe reservoirs and fluidics to deliver the fluorophore labeled probes to the array. Iterative probing in some cases also requires a thermoregulatory system or other denaturing system such that probes may be melted off of their binding targets subsequent to visualization.
  • Annealed probes are beneficially visualized by delivery of excitation energy to the probes, such that their fluorophores may be induced to emit energy of wavelengths suitable for target site identification.
  • some systems comprise electromagnetic energy generators, such as lasers or other optic systems, to deliver excitation energy to annealed probes.
  • some systems comprise an image capture functionality so as to capture emission energy such as visible light or energy of other detectable wavelengths. This image capture functionality is in some cases built into the systems. Alternately, some image capture functionality is provided externally, such as by a handheld imaging device such as a phone camera.
  • Captured images are processed either using a processor in the system, or through transmission of image data to an external imaging processing device.
  • Such a device may assign temporally distinct signals to common positions on the array, and may assign the positions to a sample and target analyte identity based upon wavelength or wavelengths detected.
  • a processor may further aggregate the data so as to provide output data relating to analyte presence in the sample.
  • a dynamic range of analyte quantification of at least 1x, 20x, 50x, 100x, 200x, 500x, 1000x, 2000x, 5000x, 10,000x, 20,000x, 50,000x, 100,000x, 200,000x, 500,000x, 1,000,000x, 2,000,000x, 5,000,000x, 10,000,000x or greater.
  • a high number of samples or probes may be concurrently assayed, Ref. No.
  • VDN.001WO such as at least 10, 20, 50, 100, 200, 500 or more than 500, or any value spanned by or falling outside of the listed range.
  • Systems herein in some cases comprise arrays harboring qualitative or quantitative information regarding one or more of a broad range of analytes, such as proteins, small molecules, transcripts, DNA and even DNA configuration in chromatin, for example. These analytes may be assayed from the same or different samples, can comprise and can be quantified across a logarithmic range of 6-8, relating to 500 or more samples concurrently.
  • Systems disclosed and contemplated herein find utility due to their ease of use, small benchtop footprint, diversity of targetable analytes and speed of use.
  • kits relating to practice of the methods and use of the compositions and systems disclosed above. Some such kits comprise one or more of the reagents discussed above, such as linear analyte probes, fluorophore labeled probes, oligo-labeled beads, patterned arrays, or other reagents consistent with the compositions, methods and systems of the disclosure herein.
  • kits comprise linear analyte probes direct to biochemically disparate targets implicated in a common disease or set of diseases, such as one or more of proteins implicated in a disease, transcripts implicated in the disease, chromatin loci implicated in a disease, metabolites implicated in a disease, or other analytes relevant to an analysis.
  • Some kits comprise linear analyte probes direct to biochemically disparate targets implicated in a broad range of disorders, diseases or health status indicators.
  • Thes kits used in combination with the systems or methods disclosed herein facilitate the rapid assessment of a broad range of health status indicators through a common system, such that 500 or more analytes may be assessed in a single assay in no more than 1-4 hours or less.
  • arrays comprising data informative of a plurality of analyte types, such as proteins, metabolites, RNA, DNA such as nuclear chromosomes, mitochondrial DNA, chloroplast DNA, pathogen DNA such as eukaryotic pathogen, bacterial pathogen or vial DNA, chromatin status, or other analytes that may be assayed from a simple sample such as a homogenous human sample or a complex sample such as a human gut metabolome or environmental sample.
  • the arrays allow comparison of analyte levels over a dynamic range of up to 6-8 orders of magnitude, for up to 500 samples Ref. No.
  • VDN.001WO or more without using fluorophore labeled analyte specific probes. Data are generated in some cases in no more than 1-4 hours or less.
  • a number of analysis methods are enabled through the use of an efficient, fast, common analyte detection and quantification workflow as disclosed herein. In particular, broad ranges of distinct analytes may be detected through a common assay. The number of analyte types to be detected is in some cases limited not by the size of the array but by the number of fluorophores and (or raised to the power of) the number of rounds of analyte detection.
  • These analytes may comprise a broad range of subjects, such as proteins, protein aggregates, protein phosphorylation or other modification states small molecule metabolites, carbohydrates, lipids or other cellular components, transcripts such as mRNA or other RNA molecules, DNA molecules such as DNA loci having sequence mutation or variability of interest, telomer lengths (as measured, for example, by quantity of annealing probes), chromatin status such as chromatin DNA accessibility or chromatin protein modification status, or other analytes or states.
  • subjects such as proteins, protein aggregates, protein phosphorylation or other modification states small molecule metabolites, carbohydrates, lipids or other cellular components, transcripts such as mRNA or other RNA molecules, DNA molecules such as DNA loci having sequence mutation or variability of interest, telomer lengths (as measured, for example, by quantity of annealing probes), chromatin status such as chromatin DNA accessibility or chromatin protein modification status, or other analytes or states.
  • any molecule or molecule modification state that may be bound by an antibody, receptor, ligand or other binding moiety that may be tagged by a guide, or any molecule that may serve as a guide or may serve as a template for guide synthesis (via transcription or polymerase chain reaction for example) may serve as an analyte through the systems herein.
  • analytes or their output signals are readily collected as parts of a common array output, facilitating comparisons among or across sample runs. This facilitates rapid, accurate collection and comparison of outputs corresponding to a broad range of biomarkers relating to one or a plurality of phenotypes, conditions or states.
  • the ease of use of some systems herein is conducive to the long-term or temporally distinct use in collection of data across multiple timepoints, as may be accomplished by a home user or a used at a site where tests are administered.
  • one may monitor protein levels and phosphorylation or other modification states, transcript accumulation levels, mitochondrial activity, mitochondrial health or mitochondrial integrity, chromatin configuration and any number of other analytes relating to a status. These are readily, comparably measured at one or a plurality of time points, over a course such as a chemotherapy treatment regimen, a retroviral treatment regimen, an aging time course or an untargeted health monitoring regimen.
  • a type of analyte assay compatible with the systems, methods and compositions disclosed herein.
  • the assay detects and quantifies accessible portions of chromosomes packed into chromatin.
  • Histones depicted as circular particles twice wrapped by DNA, render the majority of the chromosome inaccessible.
  • a single gap, labeled “accessible chromatin” is not rendered inaccessible by the histones.
  • the chromatin is contacted to transpososomes or transposases loaded with transposon ends having RNA polymerase promoter sites fused thereto.
  • the transposon ends have primer binding sites compatible with PCR amplification in place of or in addition to the RNA polymerase promoter sites.
  • the chromatin is subjected to transposition, gap filling, and transcription so as to generate RNA transcripts templated by the region of the chromosome that is accessible to the transposase. This is shown at bottom left, in the section marked “B” of Fig. 1.
  • the sample is contacted to a population of linear analyte probe nucleic acids, some of which having 5’ and 3’ ends reverse complementary to at least some of the RNA transcripts, such that the RNA transcripts serve as guides to bring the 5’ and 3’ ends of the linear analyte probe into proximity.
  • PCR amplicons or oligos tagged to antibodies, receptor or ligand proteins, or aptamers, among others, may serve as guides. This is shown at top center, in the section marked “C” of Fig. 1.
  • the linear analyte probe is contacted to a DNA ligase under conditions sufficient for ligase to occur, such that the linear analyte probe is circularized to form a circular analyte probe. This is depicted in the middle center of Fig. 1, at the section labeled “D”.
  • a wash step DNA exonuclease step, RNase treatment step melting step or other processing to remove unligated linear analyte probe nucleic acids, ligase and ligation buffer, transposase, RNA polymerase, and cleaved and uncleaved chromosome and chromatin fragments.
  • ligase and ligation buffer ligase and ligation buffer
  • transposase RNA polymerase
  • RNA polymerase cleaved and uncleaved chromosome and chromatin fragments.
  • oligo labeled solid surfaces as those of a microparticle or bead population.
  • the oligos of the surface are reverse complementary at their 3’ ends to a portion of the circular analyte probes that is in many cases invariant across samples and target analytes.
  • the oligos are tethered to an array directly.
  • the complexed circular analyte probes are then used to template a DNA polymerase catalyzed extension reaction off of the primer 3’ end, so as to effect rolling circle amplification of the bound circular analyte probe to form a concatemer of the circular analyte probe tethered to the bead. This is shown in the section labeled “F” of Fig. 1.
  • the beads are delivered to a pattered array and deposited into wells of the array, as shown in the lower file of Fig. 1 adjacent to the letter “G”.
  • the concatemers are then iteratively probed using fluorophore-labeled probes that bind to regions of the concatemers that correspond to sample markers, analyte markers and optionally other markers.
  • fluorophore-labeled probes that bind to regions of the concatemers that correspond to sample markers, analyte markers and optionally other markers.
  • individual binding and detection events do not provide specificity to identify particular analytes in a single round, so multiple iterative rounds using distinct probes or color patterns are used to generate sequential ‘barcode’ fluorescence patterns that may be used to identify the circular analyte probe concatemer corresponding to a particular position on the array.
  • photobleaching is used to remove fluorescence signals between iterative probe binding rounds.
  • probes may be removed via melting.
  • probes are used to prime sequencing by extension reactions, such as sequencing by synthesis r sequencing by binding, so as to determine particular sequence segments of the concatemerized circular analyte probes at particular points on the array.
  • the method comprises the following steps: Ref. No. VDN.001WO [0086] Permeabilize cells or nuclei in the bio samples, followed by treatment of a DNA transposases coupled with a DNA oligo adaptor, which breaks the double stranded DNA at nucleosome free regions and simultaneously ligates the DNA oligo adaptors to the ends of DNA breaks.
  • the DNA oligo adaptor contains a sequence that can be recognized by RNA polymerase such as T7 ( Figure 1a).
  • RNA polymerase such as T7 ( Figure 1a).
  • RNA molecules (a few hundred nucleotides in length on average) at the sites of transposon insertion.
  • the sequences of the RNA molecules correspond to the immediate adjacent sequences to the transposase insertions and could be used as template for subsequent hybridization to padlock probes described in the following step.
  • the number of the RNA molecules produced at each site depends linearly on the reaction time and could reach hundreds or thousands of copies ( Figure 1b).
  • Segment #2 is a DNA sequence unique to each predefined target sequence and is referred to hereafter as the barcode sequence.
  • Segment #3 is a common sequence referred hereafter as the primer sequence ( Figure 1c). The order of segments #2 and #3 could be reversed.
  • a ligation reaction is then carried out with each sample, such that the linear DNA molecules that have been hybridized to the target RNA molecules with the complementary sequences are circularized. This step typically involves the use of T4 ligase or its variants, but other ligases could be used as well (Figure 1d).
  • VDN.001WO Quantify the abundance of each DNA barcode (segment #2) on the surface by sequentially hybridizing fluorescence tagged oligonucleotides corresponding to a part of the DNA barcode sequence. Fluorescence images are taken after each round of hybridization and then aligned to each other. The combinations of fluorescence signals at each location on the surface are used to decode the DNA barcodes. The numbers of each types of DNA barcodes are then counted, to measure the chromatin accessibility at the corresponding target DNA sequences in the bio samples ( Figure 1g).
  • step (a) the biospecimens could be incubated with transposases Tn5, which could generate double-stranded DNA breaks while also ligating an DNA oligo adaptor the ends of DNA breaks.
  • the DNA oligonucleotide adaptors could be gap-filled with DNA polymerases before the next step.
  • the bio samples could be processed with SDS and/or proteinase K to remove nucleosomes and Tn5 transposases from the DNA. DNA might be further extracted before the next step.
  • DNA molecules described in step (c) could contain more than 4 segments.
  • step (e) the DNA circles could be released under denaturing conditions, or exonuclease digestion, or RNase H digestion of RNA in the RNA/DNA hybrids. [0097] Step (e) could also be skipped. [0098] In step (e-f), the DNA circles on the biosamples (or tissue slices) could come directly in contact with a surface coated with oligonucleotides. This would enable spatially resolved assessment of chromatin accessibility in the biosamples. [0099] In step (f) the DNA circles could hybridize to patterned DNA microarrays. [0100] The said DNA microarrays could comprise beads arrays.
  • Beads with diameters that range from sub 10nm to hundreds of microns and based on such materials as but not limited to silica, polystyrene, and magnetic particles.
  • DNA oligonucleotide with predefined sequences immobilized on the beads. The oligonucleotides contain a section of sequence complement to the primer sequence (#3 on the DNA circles).
  • Patterned substrates manufactured by such methods but not limited to Photolithography and plasma etching, Nanoimprinting, Hot embossing, or other approaches in the art.
  • the substrate can be silicon or glass
  • the substrate can be fabricated on CMOS.
  • Bead loading onto patterned substrate is accomplished by Physically loading the beads into micro/nanowell patterned substrate (push beads into patterns by mechanical force). Ref. No. VDN.001WO [0105] The identity of the DNA oligonucleotides is decoded by iteratively delivering and annealing probes to the concatemerized circular analyte probe sequence tethered to the beads. Despite having far fewer fluorophores than the diversity of the analytes detected, through iterative detection one may identify and quantify individual probes. [0106] Decoding of DNA oligonucleotide on each Bead to generate a map for different probes on different locations on the substrate. Example 2. Complex sample analysis.
  • a tumor sample is obtained from an individual suffering symptoms of an unknown cause.
  • the sample is assayed for known viral, bacterial and eukaryotic pathogens, circulating free DNA, and white and red blood cell status.
  • the sample is collected in a hospital, and the patient is then taken for examination by a health care provider. During the appointment, the sample is analyzed using a system as disclosed herein.
  • the sample is probed for levels of human and pathogen transcripts, chromatin configuration, and protein levels.
  • guide labeled chromatin constituents are added, so as to assay for levels of chromatin binding moieties.
  • the sample is found to show normal levels of human cellular proteins assayed for, and no heightened level of known pathogens in the tumor.
  • transcripts A subset of transcripts is observed to accumulate at higher levels than expected, and these transcripts are found to correspond to a chromatin region that is indicated to be in an aberrant configuration. Chromatin constituents associated with that region are found to bind to an unknown moiety. The identity of the moiety is not determined, but the moiety is determined to be present in the sample at a level comparable to the degree of chromatin configuration aberration. [0109] The data is available to the medical practitioner during the examination by the health care provider. The provider concludes that the tumor may be related to activity of an unknown moiety acting on chromatin constituents so as to reconfigure expression of genes in the vicinity of the region in aberrant configuration. Example 3. Independent measurements do not facilitate comparisons.
  • a sample is taken from an individual and analyzed using approaches in the art. Transcriptome, proteome and chromatin configuration data are obtained. The data from separate assays qualitatively indicate that a protein is upregulated, that its corresponding transcript is upregulated, and that the gene encoding the transcript is differentially available in chromatin of the individual. The magnitude of the differences cannot be compared due to the distinct systemic biases in the disparate data collection approaches.
  • a sample is taken from an individual and analyzed using systems of the disclosure herein. Transcriptome, proteome and chromatin configuration data are obtained from a single array using a common analysis workflow, so as to facilitate data comparisons.
  • the data indicate that a protein is upregulated, that its corresponding transcript is upregulated, and that the gene encoding the transcript is differentially available in chromatin of the individual.
  • the magnitude of the differences suggest that the protein is 100x upregulated, while the transcript is slightly upregulated, and the chromatin reconfiguration event occurs only sporadically in the sample.
  • a medical professional concludes that the upregulation in protein accumulation levels may be a result of increased recruitment of the transcript to the ribosome or from decreased turnover of the protein specifically, resulting in increased protein accumulation.
  • the levels of transcript accumulation and of chromatin reconfiguration when viewed in comparison to the protein accumulation levels, suggest that the defect does not rest with chromatin configuration or transcript accumulation.
  • Example 5 This example, viewed in combination with Example 3, illustrates the benefit of assessing multiple analytes through a common workflow so as to generate quantitatively relatable data.
  • Example 5 Health analysis kits. [0115] A kit is provided having linear analyte probes for use in systems disclosed herein.
  • the kit comprises linear probes directed to proteins, metabolites, transcripts, DNA mutations, and chromatin configuration changes implicated in various health related topics, such as arthritis, Alzheimer’s progression, amyloid or other age related protein misfolding, telomere length, T cell senescence, organellar activity, damaged protein accumulation or aggregation, autophagy activity, sirtuin activity, TOR signaling, epigenetic modifications, DNA methylation, histone landscape analysis, stem cell status, inflammation pathway activity, apoptosis and other age related health topics.
  • the kit is used with a system herein to obtain data related to proteins, metabolites, transcript accumulation and splicing information, DNA sequence information and chromatin structural information.
  • the data are obtained concurrently, through a sample processing pipeline that converges at the level of analyte detection and that provides readily comparable quantitative data across analytes.
  • the kit is used on an individual showing signs of aging. The data indicates that certain aging related pathways, such as inflammation and telomere length, appear normal, while Ref. No. VDN.001WO SIRTUIN/TOR signaling appears defective. The individual adopts a caloric restriction diet that perturbs SIRTUIN/TOR signaling, and observes an alleviation in age-related symptoms.
  • Example 6. Cancer stage characterization [0119] A patient is subjected to a routine cancer check and a tumor is detected.
  • the tumor is subjected to standard, separated assays and is determined to have an oncogenic protein.
  • the tumor is subjected to an assay through the systems disclosed herein and it is determined that the tumor cells exhibit a chromatin conformation consistent with pre- metastatic status, slight transcriptome aberrations and expression of the oncogenic protein at low levels.
  • the tumor is determine to be early stage and non-metastatic, and is treated by a localized intervention rather than through a much more traumatic systemic therapeutic regimen.
  • a patient is found to have cancer warranting chemotherapeutic intervention.
  • An assay as disclosed herein is performed and the patient is found to have transcripts and proteins indicative of metastasis, and to have chromatin configurations consistent with advanced cancer.
  • the patient undergoes chemotherapy to clear the cancer cells. Ongoing monitoring indicates that the transcripts and proteins indicative of metastasis steadily decline concurrently with treatment.
  • the treatment regimen is completed. Monitoring indicates that transcripts and proteins indicative of metastasis have returned to healthy levels, and the patient ceases to exhibit symptoms of cancer warranting intervention.
  • Monitoring also indicates that the patient still exhibits chromatin configurations consistent with advanced cancer.
  • a follow-up treatment is selected to target tumor cells not cleared by the chemotherapy treatment regimen, and the cancer is cleared.

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Abstract

Methods, compositions, kits, datasets and systems relating to the detection and quantification of disparate analytes are disclosed herein. This disclosure facilitates the concurrent, rapid, accurate quantification of biochemically disparate analytes, such as proteins, metabolites, RNA, DNA, and chromatin configuration, for example, in an assay workflow having a large number of common assay steps and a common output, such that measurement of these disparate analytes is rapidly and accurately accomplished, and comparisons readily made without concern for systemic bias and without need for distinct detection systems.

Description

Ref. No. VDN.001WO UNIFIED DETECTION WORKFLOW CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This document claims the benefit of priority to US Prov Ser No 63/494,693, filed April 6, 2023, and to US Prov Ser No 63/494,695, filed April 6, 2023, the contents of each of which are hereby incorporated by reference in their respective entireties. BACKGROUND [0002] Many biological questions are informed by information gathered at multiple levels, such as at the levels of proteomic information, chromatin configuration information, transcript accumulation information and genomic sequence information. However, data gathering is often siloed, such that various levels of information or data are gathered by distinct approaches. [0003] For example, proteins may be assayed using primary and secondary antibody based approaches, while transcriptomes and genomes are assessed, and chromatin configuration assayed through distinct library preparation and sequencing approaches or through more disparate techniques. [0004] If one is to access data obtained through multiple distinct approaches, one requires a plurality of distinct skill sets and tools to generate the various categories of data, as well as distinct understanding of the biases in each data collection approach so that their outputs may be properly assembled so as to inform or answer these multileveled questions. SUMMARY [0005] Disclosed herein are compositions, systems and methods relating to accumulation of multi-level biological data through a single set of tools, techniques and outputs. Through the practice of the disclosure herein, one can generate through a single device, using a single set of techniques, data from a sample or a plurality of samples relating to a broad range of analytes, such as proteins, RNA accumulation levels, DNA sequence, chromatin configuration, or other levels of information relevant to understanding, diagnosing or addressing a broad range of biological questions. [0006] Central to many of these compositions, systems and methods are molecular mechanisms comprising analyte based probe circularization, followed by annealing of circularized probes to probe-binding primers on a solid particle such as a microbead so as to anchor the rolling circle amplification of the circularized probes. The solid particles are Ref. No. VDN.001WO deposited into positions such as wells on an array, at which they can be probed using sample specific, analyte type specific, analyte specific or other probes so as to identify the analyte corresponding to an RCA amplicon tethered to a bead at a particular position on the array. Probes may be assayed using fluorescence detection, and detection may comprise single probe detection or multiple rounds of annealing by distinct probes so as to generate temporal fluorescence patterns corresponding to particular circularized probes or analytes that their circularization indicates. [0007] A partial list of further embodiments of the disclosure is presented below. Some embodiments, such as embodiment 1, relate to methods, such as methods for detecting an analyte or a plurality of analytes, of similar or difference chemical characteristics, said methods comprising one or more of the steps of generating a circular nucleic acid indicative of an analyte in a sample; annealing the circular nucleic acid to a surface oligo of a microparticle comprising a plurality of surface oligos; contacting the circular nucleic acid to a polymerase, dNTPs and a buffer consistent with nucleic acid extension; extending the surface oligo to form a concatemer of the circular nucleic acid tethered to the microparticle; depositing the microparticle in a well of a microarray; contacting the microarray to a first probe; and assaying for a signal indicative of the first probe bound to the concatemer. 2. The method of any previous embodiment, such as embodiment 1, wherein generating the circular nucleic acid indicative of an analyte in a sample comprises annealing a linear precursor nucleic acid to a guide such that the 5’ end and 3’ end of the linear precursor are held in proximity, and ligating the 5’ and 3’ ends of the linear precursor. 3. The method of any previous embodiment, such as embodiment 2, wherein the guide comprises a nucleic acid in the sample. 4. The method of any previous embodiment, such as embodiment 2, wherein the guide comprises a nucleic acid that tags an antibody targeting an analyte in the sample. 5. The method of any previous embodiment, such as embodiment 2, wherein the guide comprises a PCR amplicon from the sample. 6. The method of any previous embodiment, such as embodiment 2, wherein the guide comprises an RNA molecule transcribed from a promoter- tagged fragment of the sample. 7. The method of any previous embodiment, such as embodiment 2, wherein the guide is generated by tagmentation. 8. The method of any previous embodiment, such as embodiment 2, wherein the guide is generated by revers- transcription. 9. The method of any previous embodiment, such as embodiment 2, wherein the guide is generated by cleaving a nucleic acid of the sample. 10. The method of any previous embodiment, such as embodiment 2, wherein the guide is generated by attaching primer binding sites at ends of a nucleic acid fragment of the sample. 11. The method of any Ref. No. VDN.001WO previous embodiment, such as embodiment 2, wherein the guide is generated by attaching transcription promoter sites ad at least one end of a nucleic acid fragment of the sample. 12. The method of any previous embodiment, such as embodiment 2, wherein the guide comprises an oligo tag attached to an analyte binding moiety. 13. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises an antibody binding domain. 14. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises an antibody. 15. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises a receptor. 16. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises a ligand. 17. The method of any previous embodiment, such as embodiment 13, wherein the analyte binding moiety comprises an aptamer. 18. The method of any previous embodiment, such as embodiment 4, wherein the analyte is a protein. 19. The method of any previous embodiment, such as embodiment 1, wherein the circular nucleic acid comprises a segment indicative of the analyte in the sample. 20. The method of any previous embodiment, such as embodiment 1, wherein the circular nucleic acid comprises a segment indicative of the sample. 21. The method of any previous embodiment, such as embodiment 1, wherein the surface oligo is covalently bound to the microparticle. 22. The method of any previous embodiment, such as embodiment 1, wherein contacting the circular nucleic acid to a polymerase comprises washing the microparticle. 23. The method of any previous embodiment, such as embodiment 1, wherein extending the surface oligo to form a concatemer of the circular nucleic acid tethered to the microparticle is performed under isothermal conditions. 24. The method of any previous embodiment, such as embodiment 23, wherein said isothermal conditions comprise room temperature extension. 25. The method of any previous embodiment, such as embodiment 23, wherein said isothermal conditions comprise extension at about 70 degrees C. 26. The method of any previous embodiment, such as embodiment 1, wherein the depositing occurs subsequent to the extending. 27. The method of any previous embodiment, such as embodiment 1, wherein the depositing occurs prior to the extending. 28. The method of any previous embodiment, such as embodiment 1, wherein the microarray comprises at least 100 wells. 29. The method of any previous embodiment, such as embodiment 1, wherein the microarray comprises at least 1000 wells. 30. The method of any previous embodiment, such as embodiment 1, wherein the microarray comprises at least 10,000 wells. 31. The method of any previous embodiment, such as embodiment 1, wherein the microarray exhibits at least 90% well occupancy. 32. The method of any previous embodiment, such as embodiment 1, wherein the Ref. No. VDN.001WO microarray exhibits at least 95% well occupancy. 33. The method of any previous embodiment, such as embodiment 1, wherein the microarray exhibits at least 99% well occupancy. 34. The method of any previous embodiment, such as embodiment 1, wherein assaying for a signal indicative of the first probe bound to the concatemer comprises capturing an image of the array. 35. The method of any previous embodiment, such as embodiment 34, wherein capturing the image comprises using a portable device. 36. The method of any previous embodiment, such as embodiment 34, wherein capturing the image comprises using an optics system coupled to the array. 37. The method of any previous embodiment, such as embodiment 1, comprising removing the first probe and contacting the microarray to a second probe, and assaying for a signal indicative of the second probe bound to the concatemer. 38. The method of any previous embodiment, such as embodiment 1, wherein the method detects an analyte in the sample. 39. The method of any previous embodiment, such as embodiment 1, wherein the method quantified an analyte in the sample. 40. The method of any previous embodiment, such as embodiment 1, wherein the method detects at least 100 distinct analytes in the sample. 41. The method of any previous embodiment, such as embodiment 1, wherein the method quantifies at least 100 distinct analytes in the sample. 42. The method of any previous embodiment, such as embodiment 1, wherein the method detects at least 1000 distinct analytes in the sample. 43. The method of any previous embodiment, such as embodiment 1, wherein the method quantifies at least 1000 distinct analytes in the sample. 44. The method of any previous embodiment, such as embodiment 1, wherein the method detects at least 10,000 distinct analytes in the sample. 45. The method of any previous embodiment, such as embodiment 1, wherein the method quantifies at least 10,000 distinct analytes in the sample. 46. The method of any previous embodiment, such as embodiment 1, wherein the method is practiced on an individual at two distinct time points. 47. The method of any previous embodiment, such as embodiment 46, wherein a treatment is administered to the patient between the two distinct time points. 48. The method of any previous embodiment, such as embodiment 46, wherein a treatment is administered to the patient prior to the two distinct time points. 49. The method of any previous embodiment, such as embodiment 46, wherein a treatment is administered to the patient concurrently with at least one of the two distinct time points. 50. A system comprising components for execution of the method of any previous embodiment, such as embodiment 1. 51. The system of any previous embodiment, such as embodiment 50, configured to analyze a plurality of analytes. 52. The system of any previous embodiment, such as embodiment 50, configured to analyze a plurality of analyte types. 53. The system of any previous Ref. No. VDN.001WO embodiment, such as embodiment 50, configured to analyze a nucleic acid analyte and a polypeptide analyte. 54. The system of any previous embodiment, such as embodiment 50, configured to analyze a chromatin status. 55. A kit comprising reagents for operation of the system of any previous embodiment, such as embodiment 50. 56. A composition comprising a first microparticle having a surface coating of oligos, at least one of which is bound to a first circular nucleic acid. 57. The composition of any previous embodiment, such as embodiment 56, wherein the first microparticle is deposited in a well. 58. The composition of any previous embodiment, such as embodiment 57, wherein the well is a constituent of a patterned array of at least 100 wells. 59. The composition of any previous embodiment, such as embodiment 57, wherein the well is a constituent of a patterned array of at least 1,000 wells. 60. The composition of any previous embodiment, such as embodiment 57, wherein the well is a constituent of a patterned array of at least 10,000 wells. 61. The composition of any previous embodiment, such as embodiment 57, wherein the well is a constituent of a patterned array that exhibits at least 90% well occupancy. 62. The composition of any previous embodiment, such as embodiment 57, wherein the well is a constituent of a patterned array that exhibits at least 95% well occupancy. 63. The composition of any previous embodiment, such as embodiment 57, wherein the well is a constituent of a patterned array that exhibits at least 99% well occupancy. 64. The composition of any previous embodiment, such as embodiment 56, further comprising a polymerase, dNTPs, and a buffer suitable for nucleic acid extension. 65. The composition of any previous embodiment, such as embodiment 56, further comprising a second microparticle bound to a second circular nucleic acid. 66. The composition of any previous embodiment, such as embodiment 65, wherein the first circular nucleic acid corresponds to a first target analyte and the second circular nucleic acid corresponds to a second target analyte. 67. The composition of any previous embodiment, such as embodiment 66, wherein the first target analyte is a nucleic acid. 68. The composition of any previous embodiment, such as embodiment 67, wherein the nucleic acid has a sequence corresponding to an expressed RNA molecule. 69. The composition of any previous embodiment, such as embodiment 67, wherein the nucleic acid has a sequence corresponding to an exposed chromosomal segment of chromatin. 70. he composition of any previous embodiment, such as embodiment 67, wherein the nucleic acid has a sequence corresponding to a cancer cell transcriptome transcript. 71. The composition of any previous embodiment, such as embodiment 67, wherein the nucleic acid has a sequence corresponding to a transcript differentially expressed in response to a cell treatment. 72. The composition of any previous embodiment, such as Ref. No. VDN.001WO embodiment 67, wherein the nucleic acid has a sequence corresponding to a transcript differentially expressed in a cell cycle. 73. The composition of any previous embodiment, such as embodiment 67, wherein the nucleic acid has a sequence corresponding to a transcript differentially expressed in response to a disease. 74. The composition of any previous embodiment, such as embodiment 67, wherein the nucleic acid has a sequence corresponding to a transcript differentially expressed in a specific tissue. 75. The composition of any previous embodiment, such as embodiment 67, wherein the second target analyte is a protein. 76. The composition of any previous embodiment, such as embodiment 66, wherein the first target analyte is a protein. 77. The composition of any previous embodiment, such as embodiment 56, wherein the first circular nucleic acid comprises a sample barcode. 78. The composition of any previous embodiment, such as embodiment 56, wherein the first circular nucleic acid comprises a segment indicative of a target analyte. 79. The composition of any previous embodiment, such as embodiment 56, wherein the first circular nucleic acid comprises a segment that anneals to a target analyte. 80. The composition of any previous embodiment, such as embodiment 56, wherein the bound oligo is subjected to a polymerase extension reaction to form a concatemer of the circular nucleic acid. 81. A microparticle comprising a plurality of covalently bound surface oligos, at least one of which shares a common phosphodiester backbone with a concatemeric repeat of a circular nucleic acid molecule. 82. The microparticle of any previous embodiment, such as embodiment 81, wherein the microparticle is deposited in a microarray well of a microarray. 83. The microparticle of any previous embodiment, such as embodiment 82, wherein the microarray comprises at least 100 wells. 84. The microparticle of any previous embodiment, such as embodiment 82, wherein the microarray comprises at least 1000 wells. 85. The microparticle of any previous embodiment, such as embodiment 82, wherein the microarray comprises at least 10,000 wells. 86. The microparticle of any previous embodiment, such as embodiment 82, wherein the microarray exhibits at least 90% well occupancy. 87. The microparticle of any previous embodiment, such as embodiment 82, wherein the microarray exhibits at least 95% well occupancy. 88. The microparticle of any previous embodiment, such as embodiment 82, wherein the microarray exhibits at least 99% well occupancy. 89. The microparticle of any previous embodiment, such as embodiment 81, comprising a probe bound to a repeating segment of the concatemeric repeat. 90. The microparticle of any previous embodiment, such as embodiment 89, wherein the probe comprises a fluorophore. 91. The microparticle of any previous embodiment, such as embodiment 89, wherein the repeating segment comprises a sample identifying sequence. 92. The microparticle of any Ref. No. VDN.001WO previous embodiment, such as embodiment 89, wherein the repeating segment comprises a target analyte identifying sequence. 93. The microparticle of any previous embodiment, such as embodiment 89, wherein the repeating segment comprises a target analyte sequence. 94. The microparticle of any previous embodiment, such as embodiment 89, wherein the repeating segment comprises a microparticle surface oligo binding sequence. 95. An array comprising a plurality of wells, at least some of the wells each harboring no more than one nanoparticle per well, wherein the nanoparticles comprise covalently surface bound oligos, and wherein at least a portion of the nanoparticles are bound to circular reporter nucleic acids. 96. The array of any previous embodiment, such as embodiment 95, wherein the circular reporter nucleic acids comprise circular reporter nucleic acids corresponding to target nucleic acids. 97. The array of any previous embodiment, such as embodiment 95, wherein the circular reporter nucleic acids comprise circular reporter nucleic acids corresponding to tags indicative of target analytes. 98. The array of any previous embodiment, such as embodiment 95, wherein the circular reporter nucleic acids comprise a first population of circular reporter nucleic acids corresponding to target analyte nucleic acids and a second population of circular reporter nucleic acids corresponding to target analyte polypeptides. 99. The array of any previous embodiment, such as embodiment 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from a single sample. 100. The array of any previous embodiment, such as embodiment 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least two samples. 101. The array of any previous embodiment, such as embodiment 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least 10 samples. 102. The array of any previous embodiment, such as embodiment 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least 100 samples. 103. The array of any previous embodiment, such as embodiment 95, wherein the circular reporter nucleic acids comprise sample barcodes. 104. The array of any previous embodiment, such as embodiment 97, wherein the circular reporter nucleic acids comprises target analyte identifying barcodes. 105. The array of any previous embodiment, such as embodiment 98, wherein the circular reporter nucleic acids comprises target analyte identifying barcodes. 106. The array of any one of any previous embodiment, such as embodiments 95 - 105, wherein the circular reporter nucleic acids are tethered to the at least a portion of the nanoparticles through the surface bound oligos. 107. The array of any one of any previous embodiment, such as embodiments 95 - 105, wherein at least some of the surface oligos are extended to comprise concatemeric repeats of circular reporter nucleic Ref. No. VDN.001WO acids. 108. The array of any previous embodiment, such as embodiment 95, wherein at least some of the surface oligos are extended to comprise concatemeric repeats of circular reporter nucleic acids. 109. The array of any previous embodiment, such as embodiment 108, comprising a first population of probes bound to the concatemeric repeats of the circular nucleic acids. 110. The array of any previous embodiment, such as embodiment 95, wherein at least some of the plurality of wells are occupied. 111. The array of any previous embodiment, such as embodiment 95, wherein at least 90% of the plurality of wells are occupied. 112. The array of any previous embodiment, such as embodiment 95, wherein at least 95% of the plurality of wells are occupied. 113. The array of any previous embodiment, such as embodiment 95, wherein at least 99% of the plurality of wells are occupied. 114. A dataset comprising data generated through the method of any previous embodiment, such as embodiment 1, wherein the dataset comprises nucleic acid data, polypeptide data. 115. The dataset of any previous embodiment, such as embodiment 114, wherein the dataset comprises analyte data for at least 100 analytes. 116. The dataset of any previous embodiment, such as embodiment 114, wherein the dataset comprises analyte data for at least 200 analytes. 117. The dataset of any previous embodiment, such as embodiment 114, wherein the dataset is generated in no more than 4 hours. 118. The dataset of any previous embodiment, such as embodiment 114, wherein the dataset is generated in no more than 1 hour. INCORPORATION BY REFERENCE [0008] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. BRIEF DESCRIPTION OF THE DRAWINGS [0009] Fig. 1 depicts a workflow for chromatin access determination. [0010] Fig. 2 depicts beads on an unpatterned surface. [0011] Fig. 3 depicts a patterned surface of unloaded wells. [0012] Fig. 4 depicts a patterned surface of wells into which beads have been loaded. DETAILED DESCRIPTION [0013] Disclosed herein are compositions systems and methods for concurrent, single mechanism monitoring of multiple types of analytes or cell state measurement such as Ref. No. VDN.001WO chromatin configuration measurements. Through practice of the disclosure herein, one may generate, on a single platform, readily comparable data relating to one or more or transcript accumulation, genomic locus sequence and copy number measurements, protein accumulation and modification, other metabolite accumulation levels, chromatin configuration or other biological information from a sample such as a single cell sample or from a plurality of samples concurrently. The data may relate to presence or absence of one or more analytes, and may also comprise quantitative measurements of analyte abundance in a sample, A large plurality of analytes or sets of analytes from common or distinct samples, such as samples subjected to distinct treatments or from individuals exhibiting distinct phenotypes, may be assayed concurrently on a single array, so as to facilitate concurrent, high throughput analysis of a broad range of analytes, analyte types and samples. [0014] A mechanism common to a broad range of analyte detection approaches is the circularization of a linear analyte specific probe as a first step or early step in analyte detection. Linear probes consistent with the disclosure herein comprise 5’ and 3’ end regions that are often selected to anneal to adjacent portions of a common guide or target. [0015] Linear probes in some cases further comprise a region that is common to a particular sample and that distinguishes linear probes applied to that sample from linear probes applied to at least one other sample. This region is in some cases a sample barcode, or sample barcode region, or sample probe binding region, as it may be assayed for by binding to a labeled oligo probe. [0016] Linear probes in some cases further comprise a region that is common to a particular organism or individual and that distinguishes linear probes applied to that organism or individual from linear probes applied to at least one other organism or individual. This region is in some cases an organism or individual barcode, or organism or individual barcode region, or organism or individual probe binding region, as it may be assayed for by binding to a labeled oligo probe. [0017] Linear probes in some cases comprise a region that is common to a particular target analyte and that distinguishes linear probes applied to that target analyte from linear probes applied to at least one other target analyte. This region is in some cases a target analyte barcode, or target analyte barcode region, or target analyte probe binding region, as it may be assayed for by binding to a labeled oligo probe. In some cases, this region is the 5’ end region, 3’ end region or a ligation product spanning the 5’ end region and 3’ end region that are often selected to anneal to adjacent portions of a common guide or target. Alternately or Ref. No. VDN.001WO in combination, linear probes may comprise a distinct region that is common to a particular target. [0018] Linear probes in some cases further comprise a random region, such as a random hexamer, heptamer, octamer, or of length such as 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater than 20 bases, that may serve as an individual linear probe identifier and that may be used in distinguishing a signal from one linear probe indicative of an analyte from a second linear probe indicative of the same analyte, such that the number of linear probes that identified a category of analyte in a sample can be quantified. These regions are assayed by hybridization to a randomer binding region, for example, or by sequencing. [0019] Linear probes in some cases comprise a region that is universal or common to a plurality of linear probes, up to all linear probes used in an experiment. This region in some cases exhibits a distinct such as a higher GC concentration or melting point when annealed to reverse complement relative to a second region or the remainder of the linear probe. [0020] Linear probes are often single stranded at their 5’ end regions and 3’ end regions. The probes may be single stranded throughout their length or may be double stranded at regions distal from the 5’ end regions and 3’ end regions. [0021] Linear probes are in some cases selected to minimize off-target annealing, for example by selecting an overall GC bias that differs from that of nucleic acids in a target sample. In some cases, linear nucleic acids have a GC content of at least or at most 20%, 30%, 40%, 50%, 60%, 70%, or 80%, or a number spanned by or outside of that range. [0022] The target is in some cases a complementary (or, more strictly speaking, reverse complementary) nucleic acid analyte target or amplification product therefrom. That is, nucleic acid targets such as DNA or RNA may serve as their own guides for detection by circular probes. Alternately or in combination, in some cases a nucleic acid analyte is subjected to amplification such that the amplification product may serve as a guide for the linear nucleic acid probe. That is, some nucleic acid analytes may be modified to add primer binding sites or RNA polymerase promoter sites at their end or ends so as to facilitate target nucleic acid analyte amplification, such that the amplification product (be it PCR product, transcript, reverse transcribed transcript or other analyte templated amplification product) serves as a guide for positioning of the linear nucleic acid probe 5’ and 3’ ends in proximity. [0023] Alternately, in some cases the guide or guide template is an oligo tag attached to a non-nucleic acid detection moiety such as an antibody, receptor, ligand, or other protein or other analyte binding partner. In these cases, the relation between the analyte and the guide sequence is arbitrary, but so long as the user knows which analyte corresponds to a given Ref. No. VDN.001WO barcode, its effect on downstream analysis is effectively identical to use of a single nucleic acid analyte as load. [0024] A broad range of sample preparation approaches are consistent with the disclosure herein. In some cases, raw samples are analyzed, as may be the case when an extracellular analyte is targeted, such as circulating free DNA or RNA, or a circulating pathogen or extracellular viral load, for example. [0025] Alternately, samples may be processed so as to make cytoplasmic, organellar or nuclear contents available for analysis. Processing may comprise cell lysis to access cytoplasmic contents such as cytoplasmic proteins, organelles or transcriptomes. In some cases, the nucleus is retained intact so as to protect chromatin structure or to exclude partially processed RNA from a transcriptome population. Alternately, the nuclear contents may be accessed by lysing or permeabilizing the nucleus of a eukaryotic sample. [0026] The disclosure herein allows access to a broad range of processing options. For example samples may be processed to isolate or enrich for intact chromatin, nuclei, mitochondria, or other cellular structures. Lipids may be assayed for accumulation or modification status, proteins may be assayed for accumulation levels, modification status such as phosphorylation status, or activity on a substrate. [0027] Samples may be subjected to a broad range of processing steps prior to assaying. Nucleic acids may be modified to facilitate polymerase chain reaction amplification, for example by adding one or more primer binding sites. Alternately or in combination, sample nucleic acids can be modified by the addition of a promoter so as to drive transcription of a target region. Samples may be denatured, reverse transcribed, fixed, homogenized, phosphatase treated, tagmented, or subjected to any of a number of preparation approaches that are suitable for the analyte being assayed, without losing the ability to subject them to a common downstream analysis workflow. [0028] Independent of the reactions to which the sample is subjected, localization of the linear nucleic acid probe 5’ and 3’ ends by the guide facilitates circularization of the linear analyte probe. Circularization is often effected by addition of a ligase and suitable buffer to a sample in which a guide and a linear nucleic acid probe are found or could potentially be found. [0029] Conceptually, the circularized analyte probe is the common currency of many of the approaches herein. That is, circularization, be it through analyte binding to a guide tagged probe or through association with a natural or arbitrarily assigned guide or amplification product, is a first step in detection of any number among a broad range of analytes. Ref. No. VDN.001WO Furthermore, it facilitates the common downstream analysis workflow that allows common analysis of a broad range of disparate analytes. [0030] Independent of the analytes being assayed, one may adopt a common set of post- ligation processing steps in analyte analysis. [0031] Samples are in some cases processed to extract nucleic acids, DNA or circular DNA, or to degrade all but nucleic acids, DNA or circular DNA. That is, in some cases samples are processed to extract nucleic acids. Alternately or in combination, in some cases samples are treated with, for example, one or more of a protease, an RNase or a DNA exonuclease, so as to remove sample constituents other than circular DNA. Sample treatment may also comprise heat treatment for inactivation of ligase activity or denaturation of circularized analyte probes from their guides. [0032] Circularized analyte probes may then be analyzed, with their detection serving as a proxy for analyte presence or abundance. [0033] Some detection approaches comprise binding circularized analyte probes to a solid anchor or solid anchors such as a microparticle or bead population. Exemplary beads comprise silica, polymer, magnetic material, metal or metal oxide. Magnetic beads, in particular, facilitate or are conducive to physical manipulation. Beads range in size from less than 20 nm to 500 um in diameter or more, such as 10nm, 20nm, 50nm, 100nm, 200nm, 500nm, 1um, 2um, 5um, 10um, 20um, 50um, 100 um, 200um, 500um, any diameter spanned by or outside of the mentioned range. [0034] Often, circular analyte probes are contacted to an excess of beads, such that beads have no more than one circular nucleic acid attached per bead. In alternate cases, beads are provided at concentrations or amounts so as to promote high bead occupancy by circularized analyte probes. [0035] Beads are processed to have a coating of one or more oligonucleotides, such as oligonucleotides that anneal to or are the reverse complement of the universal region of the circularized analyte probes. The oligos are configured to be bound to the beads at their 5’ ends, or such that their 3’ ends are exposed and available for priming of 5’ to 3’ DNA synthesis. [0036] Accordingly, upon contacting circular analyte probes to the beads, the circular analyte probes anneal to the oligonucleotides such that a circular analyte probe is tethered to a bead via the bead surface oligonucleotide. In some cases, beads are configured to anneal to or become bound to a single circularized analyte probe, while in alternate cases beads are configured to accommodate a plurality of circularized analyte probes. Ref. No. VDN.001WO [0037] Following or concurrently with contacting of beads to circular analyte probes, the beads are contacted to DNA extension reagents such as DNA polymerase, dNTPs, and buffer conditions sufficient to support DNA polymerization. The bead oligo 3’ ends are then used to prime rolling circle amplification of bound circularized analyte probes, such that a concatemer of the circularized analyte probe is linked by a common phosphodiester backbone to the primer, and through the primer to the bead surface. Rolling circle amplification is performed through an incubation step of, for example, no more than or no less than 1, 2, 3, 4, 5, 10, 15, 30, 60 or more than 60 minutes. [0038] Having transferred the information form the circular analyte probes to the bead surface, the circular analyte probes are then separated and, in some cases, discarded, and the beads are retained for further processing. [0039] The beads are then contacted to a surface, such as a surface having patterned wells. The wells are in some cases configured so as to accommodate one bead per well. The beads are allowed to settle into the wells, or may be drawn into the wells for example using magnetic attraction, and the structure is in some cases washed to remove other reagents or unsettled beads. [0040] Wells are selected to have a size to accommodate no more than one bead at a time. Exemplary wells are about 10% larger than the bead they are configured to harbor. In some embodiments, using for example a 1um pitch, one observes more than 1 million wells per square millimeter such that there are more than 100 million wells on a 10mmx10mm chip. [0041] Beads are loaded onto the surface so as to achieve a high rate of occupancy. Various embodiments exhibit occupancy rates of at least 70%, 80%, 85%, 90%, 91%, 92% 93% or greater than 93%. [0042] Alternately, in some cases beads are allowed to pack onto an unpatterned surface. In yet further variants, primers are packaged into hydrogel beads that are printed onto a surface. [0043] A number of approaches may be used to visualize the rolling circle concatemers tethered to beads arrayed on a surface as disclosed herein. In some cases sequencing oligos and other sequencing reagents are delivered to the beads and sequencing reactions, such as sequencing by synthesis, sequencing by binding or other sequencing by extension approach is used to determine the sequence of various regions of the concatemers, such as the sample region, organism or individual region, target analyte region, and randomer region. [0044] Alternately, in some cases rolling circle concatemers are identified via probing, such as with fluorescently labeled or otherwise labeled probes. In some cases, the probes correspond completely with the regions on the rolling circle concatemers to be assayed. In Ref. No. VDN.001WO some of these cases, each region variant is assigned a distinct color for the fluorophore attached to the probe used to detect it, such that emission wavelength upon binding and excitation corresponds with the identity of the probed region. [0045] Alternately, in some cases probes span a subset of the region to which they are directed, such that multiple partially overlapping or nonoverlapping probes may be used to probe a single region. In these cases, a particular region to be probed, in combination with a subset of fluorophores tethered to probes temporally delivered to bind various subsections of the region, can specify a temporal pattern of fluorophore excitation that can specify the region without requiring a distinct fluorophore for each distinct region to be concurrently assayed. Alternate to temporal delivery of probes, multiple probes may be bound concurrently such that a color or wavelength combination is generated through the concurrent excitation of the probes’ attached fluorophores. [0046] Alternately or in combination, in some cases targets are iteratively probed using populations of probes that anneal to common target but that may differ from one another in their fluorophore label across rounds. By specifying the pattern of fluorophores designated to be brought to a particular concatemer binding site by being attached to probes that target or anneal to the binding site in iterative rounds of hybridization, one may achieve specificity in concatemer binding site detection without having a unique fluorophore for each annealing site. Rather than relying upon a single fluorophore to specifically identify a concatemer, one may specify a distinguishing or unique patter of fluorophores, according to their selected order of delivery over multiple rounds, such that concatemers may be distinguished according to their fluorescence patters observed over multiple rounds of hybridization. Using such an approach, one may distinguish a number of concatemers corresponding to the number of fluorophores, raised to the power of the number of iterative rounds of hybridization. Such an approach dramatically increases the detection diversity for an array without requiring a corresponding fluorophore diversity. [0047] An example of such an approach is disclosed in Gunderson, et al. (2004) “Decoding Randomly Ordered DNA Arrays” Genome Research 14:870-877, published online before print April 2004 and which is hereby incorporated by reference in its entirety. [0048] A benefit of these approaches is that circular analyte probe identification specificity can be achieved that far surpasses the diversity of the fluorophore population used to label the probes. This advantage is particularly pronounced when a high number of samples or probes are concurrently assayed, such as at least 10, 20, 50, 100, 200, 500 or more than 500, or any value spanned by or falling outside of the listed range. Ref. No. VDN.001WO [0049] By successively or concurrently assaying the array onto which the beads are deposited, one may establish for each position the sample, organism or individual of origin, analyte to be detected, and in some cases the number of distinct instances of binding of a particular analyte. [0050] Alternately, the number of analytes in a sample may be determined by counting the number of positions corresponding to the analyte sharing a common sample tag or sample indicator. [0051] Through the systems herein, one may obtain a dynamic range of analyte quantification of at least 1x, 20x, 50x, 100x, 200x, 500x, 1000x, 2000x, 5000x, 10,000x, 20,000x, 50,000x, 100,000x, 200,000x, 500,000x, 1,000,000x, 2,000,000x, 5,000,000x, 10,000,000x or greater. This dynamic range is accomplished independent of the analyte, such that proteins, metabolites, RNA, DNA, chromatin configuration or any other analyte to which a guide sequence can be assigned or attached may be assayed, comparably to other analytes, on a single surface. [0052] A feature of the disclosure herein is that it can lead to rapid, high throughput analyte detection. Iterative probing and detection performed on a rolling circle concatemer population may comprise in some cases 5-10 detection cycles, depending on the number of samples or other factor, each cycle comprising probe hybridization (5min) and washing (1min), scanning (10min) and dehybridization (5min), for a cycle time of around 20 minutes. Various embodiments exhibit cycle times of, for example, no more than or no less than 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, or more than 30 minutes. [0053] Consistent with the disclosure herein are systems for practice of one or more of the steps above. Early steps in the process disclosed herein may be performed on slides or in a sample chamber such as a flow cell or in microtubes or emulsions, and may be performed individually by hand or in a high throughout automated system. Such a system variously comprises distinct or common reservoirs for liner analyte probe populations, sample prep reagent such as cell or nucleus permeabilization reagents, tagmentation enzymes such as Tn5, amplification or transcription adapters, as well as DNA polymerase, RNA polymerase, guide tagged analyte binding moieties or other reagents suitable for particular analytes to be quantified, as well as ligase and ligation buffer. Such systems may further comprise a heat block or other thermoregulatory functionality. [0054] Beads may be delivered to the flow cell in which sample processing occurs. Alternately, circularized analyte probes may be extracted from a sample processing region Ref. No. VDN.001WO and delivered to a separate region for annealing to bead primers and rolling circle amplification to form concatemers on the bead surfaces. [0055] This region may be distinct from or may be the array portion of the system. That is, beads may be decorated with rolling circle concatemer amplicons distinct from or in proximity to the array. In either case, the end result is that concatemer loaded beads are deposited into wells or onto an unpatterned surface of an array. [0056] Deposited beads are probed so as to identify one or more of their sample of origin, organism or individual of origin, target analyte detected, and this information is correlated to array position to identify and in some cases quantify the analyte indicated by the circularized analyte probes. [0057] Probing in some cases requires that the system has probe reservoirs and fluidics to deliver the fluorophore labeled probes to the array. Iterative probing in some cases also requires a thermoregulatory system or other denaturing system such that probes may be melted off of their binding targets subsequent to visualization. [0058] Annealed probes are beneficially visualized by delivery of excitation energy to the probes, such that their fluorophores may be induced to emit energy of wavelengths suitable for target site identification. Accordingly, some systems comprise electromagnetic energy generators, such as lasers or other optic systems, to deliver excitation energy to annealed probes. [0059] Similarly, some systems comprise an image capture functionality so as to capture emission energy such as visible light or energy of other detectable wavelengths. This image capture functionality is in some cases built into the systems. Alternately, some image capture functionality is provided externally, such as by a handheld imaging device such as a phone camera. [0060] Captured images are processed either using a processor in the system, or through transmission of image data to an external imaging processing device. Such a device may assign temporally distinct signals to common positions on the array, and may assign the positions to a sample and target analyte identity based upon wavelength or wavelengths detected. A processor may further aggregate the data so as to provide output data relating to analyte presence in the sample. [0061] Through the systems herein, one may obtain a dynamic range of analyte quantification of at least 1x, 20x, 50x, 100x, 200x, 500x, 1000x, 2000x, 5000x, 10,000x, 20,000x, 50,000x, 100,000x, 200,000x, 500,000x, 1,000,000x, 2,000,000x, 5,000,000x, 10,000,000x or greater. A high number of samples or probes may be concurrently assayed, Ref. No. VDN.001WO such as at least 10, 20, 50, 100, 200, 500 or more than 500, or any value spanned by or falling outside of the listed range. [0062] Systems herein in some cases comprise arrays harboring qualitative or quantitative information regarding one or more of a broad range of analytes, such as proteins, small molecules, transcripts, DNA and even DNA configuration in chromatin, for example. These analytes may be assayed from the same or different samples, can comprise and can be quantified across a logarithmic range of 6-8, relating to 500 or more samples concurrently. [0063] Systems disclosed and contemplated herein find utility due to their ease of use, small benchtop footprint, diversity of targetable analytes and speed of use. Furthermore, these systems allow accurate, directly comparable data for accumulation levels across a broad range of analyte types, from proteins and small molecules to transcripts and DNA such as specific chromatin constituents. The data are measured on a single system through a common process, facilitating direct quantitative comparison among results. [0064] Consistent with the above, disclosed herein are kits relating to practice of the methods and use of the compositions and systems disclosed above. Some such kits comprise one or more of the reagents discussed above, such as linear analyte probes, fluorophore labeled probes, oligo-labeled beads, patterned arrays, or other reagents consistent with the compositions, methods and systems of the disclosure herein. Some such kits comprise linear analyte probes direct to biochemically disparate targets implicated in a common disease or set of diseases, such as one or more of proteins implicated in a disease, transcripts implicated in the disease, chromatin loci implicated in a disease, metabolites implicated in a disease, or other analytes relevant to an analysis. Some kits comprise linear analyte probes direct to biochemically disparate targets implicated in a broad range of disorders, diseases or health status indicators. Thes kits used in combination with the systems or methods disclosed herein, facilitate the rapid assessment of a broad range of health status indicators through a common system, such that 500 or more analytes may be assessed in a single assay in no more than 1-4 hours or less. [0065] Consistent with the above, disclosed herein are arrays comprising data informative of a plurality of analyte types, such as proteins, metabolites, RNA, DNA such as nuclear chromosomes, mitochondrial DNA, chloroplast DNA, pathogen DNA such as eukaryotic pathogen, bacterial pathogen or vial DNA, chromatin status, or other analytes that may be assayed from a simple sample such as a homogenous human sample or a complex sample such as a human gut metabolome or environmental sample. The arrays allow comparison of analyte levels over a dynamic range of up to 6-8 orders of magnitude, for up to 500 samples Ref. No. VDN.001WO or more, without using fluorophore labeled analyte specific probes. Data are generated in some cases in no more than 1-4 hours or less. [0066] A number of analysis methods are enabled through the use of an efficient, fast, common analyte detection and quantification workflow as disclosed herein. In particular, broad ranges of distinct analytes may be detected through a common assay. The number of analyte types to be detected is in some cases limited not by the size of the array but by the number of fluorophores and (or raised to the power of) the number of rounds of analyte detection. These analytes may comprise a broad range of subjects, such as proteins, protein aggregates, protein phosphorylation or other modification states small molecule metabolites, carbohydrates, lipids or other cellular components, transcripts such as mRNA or other RNA molecules, DNA molecules such as DNA loci having sequence mutation or variability of interest, telomer lengths (as measured, for example, by quantity of annealing probes), chromatin status such as chromatin DNA accessibility or chromatin protein modification status, or other analytes or states. In some cases any molecule or molecule modification state that may be bound by an antibody, receptor, ligand or other binding moiety that may be tagged by a guide, or any molecule that may serve as a guide or may serve as a template for guide synthesis (via transcription or polymerase chain reaction for example) may serve as an analyte through the systems herein. [0067] Having been detected, analytes or their output signals are readily collected as parts of a common array output, facilitating comparisons among or across sample runs. This facilitates rapid, accurate collection and comparison of outputs corresponding to a broad range of biomarkers relating to one or a plurality of phenotypes, conditions or states. Similarly, the ease of use of some systems herein is conducive to the long-term or temporally distinct use in collection of data across multiple timepoints, as may be accomplished by a home user or a used at a site where tests are administered. [0068] For example, one may monitor protein levels and phosphorylation or other modification states, transcript accumulation levels, mitochondrial activity, mitochondrial health or mitochondrial integrity, chromatin configuration and any number of other analytes relating to a status. These are readily, comparably measured at one or a plurality of time points, over a course such as a chemotherapy treatment regimen, a retroviral treatment regimen, an aging time course or an untargeted health monitoring regimen. [0069] Through the ready comparability of analyte types, one may observe, for example, changes in deleterious protein accumulation levels or phosphorylation states, and even a corresponding changes in encoding transcript accumulation levels, but also observe that the Ref. No. VDN.001WO frequency of chromatin configurations in a cell population has not changed, and conclude that a treatment regimen aimed at targeting a symptom arising from the deleterious protein should be continued even though the protein levels have decreased, because the chromatin configuration that may lead to the deleterious protein expression is not yet rectified. [0070] Turning to the Figures, one sees the following. [0071] At Fig. 1, one sees a type of analyte assay compatible with the systems, methods and compositions disclosed herein. The assay detects and quantifies accessible portions of chromosomes packed into chromatin. At the upper left of Fig. 1, in the section marked “A”, one sees a schematic of chromatin assembled on a chromosome. Histones, depicted as circular particles twice wrapped by DNA, render the majority of the chromosome inaccessible. However, a single gap, labeled “accessible chromatin” is not rendered inaccessible by the histones. [0072] The chromatin is contacted to transpososomes or transposases loaded with transposon ends having RNA polymerase promoter sites fused thereto. In alternate embodiments, the transposon ends have primer binding sites compatible with PCR amplification in place of or in addition to the RNA polymerase promoter sites. [0073] The chromatin is subjected to transposition, gap filling, and transcription so as to generate RNA transcripts templated by the region of the chromosome that is accessible to the transposase. This is shown at bottom left, in the section marked “B” of Fig. 1. [0074] The sample is contacted to a population of linear analyte probe nucleic acids, some of which having 5’ and 3’ ends reverse complementary to at least some of the RNA transcripts, such that the RNA transcripts serve as guides to bring the 5’ and 3’ ends of the linear analyte probe into proximity. In alternate embodiments, PCR amplicons or oligos tagged to antibodies, receptor or ligand proteins, or aptamers, among others, may serve as guides. This is shown at top center, in the section marked “C” of Fig. 1. [0075] Immediately below, the linear analyte probe is contacted to a DNA ligase under conditions sufficient for ligase to occur, such that the linear analyte probe is circularized to form a circular analyte probe. This is depicted in the middle center of Fig. 1, at the section labeled “D”. [0076] Not shown but also present in some cases are linear analyte probes whose 5’ and 3’ ends target other regions of the chromatin which, due to being rendered inaccessible by the bound histones, do not result in guide formation. Consequently, these other linear analyte probes are not brought into a configuration where their 5’ and 3’ ends are adjacent, and they are not circularized. Ref. No. VDN.001WO [0077] At the bottom center of Fig. 1, the circularized analyte probes are separated from their guides. This section is labeled “E”. Not shown are optional steps such as a wash step, DNA exonuclease step, RNase treatment step melting step or other processing to remove unligated linear analyte probe nucleic acids, ligase and ligation buffer, transposase, RNA polymerase, and cleaved and uncleaved chromosome and chromatin fragments. [0078] At top right, one sees the circular analyte probes are contacted to oligo labeled solid surfaces, as those of a microparticle or bead population. The oligos of the surface are reverse complementary at their 3’ ends to a portion of the circular analyte probes that is in many cases invariant across samples and target analytes. In alternate embodiments, the oligos are tethered to an array directly. The complexed circular analyte probes are then used to template a DNA polymerase catalyzed extension reaction off of the primer 3’ end, so as to effect rolling circle amplification of the bound circular analyte probe to form a concatemer of the circular analyte probe tethered to the bead. This is shown in the section labeled “F” of Fig. 1. [0079] The beads are delivered to a pattered array and deposited into wells of the array, as shown in the lower file of Fig. 1 adjacent to the letter “G”. The concatemers are then iteratively probed using fluorophore-labeled probes that bind to regions of the concatemers that correspond to sample markers, analyte markers and optionally other markers. In this case, individual binding and detection events do not provide specificity to identify particular analytes in a single round, so multiple iterative rounds using distinct probes or color patterns are used to generate sequential ‘barcode’ fluorescence patterns that may be used to identify the circular analyte probe concatemer corresponding to a particular position on the array. In this case, photobleaching is used to remove fluorescence signals between iterative probe binding rounds. Alternately, probes may be removed via melting. Also, in alternate detection approaches, probes are used to prime sequencing by extension reactions, such as sequencing by synthesis r sequencing by binding, so as to determine particular sequence segments of the concatemerized circular analyte probes at particular points on the array. [0080] One observes in Fig. 1 that all steps from guide driven analyte probe circularization to detection are neutral as to the source of the guide and the identity of the analyte detected. That is, by changing the chemistry of the steps shown in the left column of the top of Fig. 1, indicated by “A” and “B”, one may assay for any number of analyte types, from proteins and small molecules that may be assayed using any guide-tagged binding moiety such as an antibody or aptamer, to RNA transcripts or DNA molecules that may serve as guides or may template guide production as shown in Fig. 1. Accordingly, a broad range of analyte types may be assayed using a common workflow, to generate readily comparable data. Ref. No. VDN.001WO [0081] At Fig. 2, one sees densely packed beads on an unpatterned surface. [0082] At Fig. 3, one sees a close-up view of a patterned array comprising wells into which beads may be deposited. [0083] At Fig. 4, one sees a patterned array comprising wells into which beads have been deposited. One observes the high rate of occupancy of the beads in the wells. EXAMPLES Example 1. Multiplexed assessment of chromatin accessibility [0084] In eukaryotic cells, the genetic materials exist in the form of chromatin fiber that folds into complex and dynamic higher order structures1. Each chromatin fiber comprises large numbers of nucleosomes, which are made up of 2 units each of histone proteins H2A, H2B, H3 and H4, as well as 147 base pairs of DNA that wraps around the histone octamers. While most DNA sequences are generally inaccessible to nucleases and DNA binding proteins due to their association with nucleosomes, certain DNA regions become devoid of nucleosomes as a result of nucleosome remodeling processing during transcription, DNA repair, replication, or other nuclear processes. Detection of such exposed chromatin regions can provide valuable information about gene regulatory processes and nuclear reorganization of chromatin fibers that typically accompany disease pathogenesis2-5. In recent years, a variety of methods have been developed to detect the accessible chromatin regions that involve the treatment of chromatin fibers in biosamples with nucleases or DNA transposases, followed by high throughput DNA sequencing or hybridization to DNA microarrays2, 6, 7. These tools have allowed the mapping of candidate gene regulatory elements in the genome that are potentially used in specific tissues or cell types, and characterization of dynamic chromatin state during development, in response to environmental cues or in disease pathogenesis. On the other hand, methods that enable highly quantitative and cost-effective assessment of a panel of target genomic regions suitable for small quantities of clinical samples are highly desired and to our knowledge do not yet exist. Here, we describe a method for multiplexed assessment of chromatin accessibility for a predefined set of genomic regions in biospecimens such as tissues, cells, biofluid (blood or plasma, for example) and other samples. This method allows highly quantitative and sensitive measurements of chromatin accessibility at select DNA sequences in bio samples, which could in turn be used as biomarkers for disease diagnosis or treatment evaluations. [0085] The method comprises the following steps: Ref. No. VDN.001WO [0086] Permeabilize cells or nuclei in the bio samples, followed by treatment of a DNA transposases coupled with a DNA oligo adaptor, which breaks the double stranded DNA at nucleosome free regions and simultaneously ligates the DNA oligo adaptors to the ends of DNA breaks. The DNA oligo adaptor contains a sequence that can be recognized by RNA polymerase such as T7 (Figure 1a). [0087] Transcribe the DNA fragments near the above breaks with the RNA polymerase in situ, after addition of nucleosides or their analogs. This step results in production of RNA molecules (a few hundred nucleotides in length on average) at the sites of transposon insertion. The sequences of the RNA molecules correspond to the immediate adjacent sequences to the transposase insertions and could be used as template for subsequent hybridization to padlock probes described in the following step. The number of the RNA molecules produced at each site depends linearly on the reaction time and could reach hundreds or thousands of copies (Figure 1b). [0088] After the termination of RNA synthesis, hybridize a pool of single stranded DNA molecules to the above RNA products. Each DNA molecule consists of a minimum of four segments: segments #1 and #4 located at the two ends are nucleotide sequences complementary to a predefined target sequence for which chromatin accessibility is assessed. Segment #2 is a DNA sequence unique to each predefined target sequence and is referred to hereafter as the barcode sequence. Segment #3 is a common sequence referred hereafter as the primer sequence (Figure 1c). The order of segments #2 and #3 could be reversed. [0089] After washing away the excess DNA molecules, a ligation reaction is then carried out with each sample, such that the linear DNA molecules that have been hybridized to the target RNA molecules with the complementary sequences are circularized. This step typically involves the use of T4 ligase or its variants, but other ligases could be used as well (Figure 1d). [0090] Release the circularized DNA molecules from the RNA transcripts and allow them to hybridize to a solid planar or 3D surface coated with DNA oligos containing a complementary sequence to the primer sequence (#3) on the DNA circles (Figure 1e). [0091] Carry out a rolling circle DNA amplification reaction, in which DNA polymerases are incubated with the DNA circles hybridized to the DNA oligos on the surface. Allow the polymerase reaction to continue for a period to achieve amplification of the DNA circles (Figure 1f). This step would result in synthesis of long strand of single stranded DNA molecules with one or more repeats of the DNA segments (#1-#4). Ref. No. VDN.001WO [0092] Quantify the abundance of each DNA barcode (segment #2) on the surface by sequentially hybridizing fluorescence tagged oligonucleotides corresponding to a part of the DNA barcode sequence. Fluorescence images are taken after each round of hybridization and then aligned to each other. The combinations of fluorescence signals at each location on the surface are used to decode the DNA barcodes. The numbers of each types of DNA barcodes are then counted, to measure the chromatin accessibility at the corresponding target DNA sequences in the bio samples (Figure 1g). [0093] In step (a), the biospecimens could be incubated with transposases Tn5, which could generate double-stranded DNA breaks while also ligating an DNA oligo adaptor the ends of DNA breaks. The DNA oligonucleotide adaptors could be gap-filled with DNA polymerases before the next step. [0094] Before step (b), the bio samples could be processed with SDS and/or proteinase K to remove nucleosomes and Tn5 transposases from the DNA. DNA might be further extracted before the next step. [0095] DNA molecules described in step (c) could contain more than 4 segments. [0096] In step (e) the DNA circles could be released under denaturing conditions, or exonuclease digestion, or RNase H digestion of RNA in the RNA/DNA hybrids. [0097] Step (e) could also be skipped. [0098] In step (e-f), the DNA circles on the biosamples (or tissue slices) could come directly in contact with a surface coated with oligonucleotides. This would enable spatially resolved assessment of chromatin accessibility in the biosamples. [0099] In step (f) the DNA circles could hybridize to patterned DNA microarrays. [0100] The said DNA microarrays could comprise beads arrays. [0101] Beads: with diameters that range from sub 10nm to hundreds of microns and based on such materials as but not limited to silica, polystyrene, and magnetic particles. [0102] DNA oligonucleotide with predefined sequences immobilized on the beads. The oligonucleotides contain a section of sequence complement to the primer sequence (#3 on the DNA circles). [0103] Patterned substrates manufactured by such methods, but not limited to Photolithography and plasma etching, Nanoimprinting, Hot embossing, or other approaches in the art. For optical based (fluorescent microscope) detection, the substrate can be silicon or glass, for electrical based detection, the substrate can be fabricated on CMOS. [0104] Bead loading onto patterned substrate is accomplished by Physically loading the beads into micro/nanowell patterned substrate (push beads into patterns by mechanical force). Ref. No. VDN.001WO [0105] The identity of the DNA oligonucleotides is decoded by iteratively delivering and annealing probes to the concatemerized circular analyte probe sequence tethered to the beads. Despite having far fewer fluorophores than the diversity of the analytes detected, through iterative detection one may identify and quantify individual probes. [0106] Decoding of DNA oligonucleotide on each Bead to generate a map for different probes on different locations on the substrate. Example 2. Complex sample analysis. [0107] A tumor sample is obtained from an individual suffering symptoms of an unknown cause. The sample is assayed for known viral, bacterial and eukaryotic pathogens, circulating free DNA, and white and red blood cell status. The sample is collected in a hospital, and the patient is then taken for examination by a health care provider. During the appointment, the sample is analyzed using a system as disclosed herein. The sample is probed for levels of human and pathogen transcripts, chromatin configuration, and protein levels. In addition, guide labeled chromatin constituents are added, so as to assay for levels of chromatin binding moieties. [0108] The sample is found to show normal levels of human cellular proteins assayed for, and no heightened level of known pathogens in the tumor. A subset of transcripts is observed to accumulate at higher levels than expected, and these transcripts are found to correspond to a chromatin region that is indicated to be in an aberrant configuration. Chromatin constituents associated with that region are found to bind to an unknown moiety. The identity of the moiety is not determined, but the moiety is determined to be present in the sample at a level comparable to the degree of chromatin configuration aberration. [0109] The data is available to the medical practitioner during the examination by the health care provider. The provider concludes that the tumor may be related to activity of an unknown moiety acting on chromatin constituents so as to reconfigure expression of genes in the vicinity of the region in aberrant configuration. Example 3. Independent measurements do not facilitate comparisons. [0110] A sample is taken from an individual and analyzed using approaches in the art. Transcriptome, proteome and chromatin configuration data are obtained. The data from separate assays qualitatively indicate that a protein is upregulated, that its corresponding transcript is upregulated, and that the gene encoding the transcript is differentially available in chromatin of the individual. The magnitude of the differences cannot be compared due to the distinct systemic biases in the disparate data collection approaches. [0111] Example 4. Concurrent measurements using the technology herein. Ref. No. VDN.001WO [0112] A sample is taken from an individual and analyzed using systems of the disclosure herein. Transcriptome, proteome and chromatin configuration data are obtained from a single array using a common analysis workflow, so as to facilitate data comparisons. The data indicate that a protein is upregulated, that its corresponding transcript is upregulated, and that the gene encoding the transcript is differentially available in chromatin of the individual. The magnitude of the differences suggest that the protein is 100x upregulated, while the transcript is slightly upregulated, and the chromatin reconfiguration event occurs only sporadically in the sample. [0113] A medical professional concludes that the upregulation in protein accumulation levels may be a result of increased recruitment of the transcript to the ribosome or from decreased turnover of the protein specifically, resulting in increased protein accumulation. The levels of transcript accumulation and of chromatin reconfiguration, when viewed in comparison to the protein accumulation levels, suggest that the defect does not rest with chromatin configuration or transcript accumulation. [0114] This example, viewed in combination with Example 3, illustrates the benefit of assessing multiple analytes through a common workflow so as to generate quantitatively relatable data. Example 5. Health analysis kits. [0115] A kit is provided having linear analyte probes for use in systems disclosed herein. The kit comprises linear probes directed to proteins, metabolites, transcripts, DNA mutations, and chromatin configuration changes implicated in various health related topics, such as arthritis, Alzheimer’s progression, amyloid or other age related protein misfolding, telomere length, T cell senescence, organellar activity, damaged protein accumulation or aggregation, autophagy activity, sirtuin activity, TOR signaling, epigenetic modifications, DNA methylation, histone landscape analysis, stem cell status, inflammation pathway activity, apoptosis and other age related health topics. [0116] The kit is used with a system herein to obtain data related to proteins, metabolites, transcript accumulation and splicing information, DNA sequence information and chromatin structural information. The data are obtained concurrently, through a sample processing pipeline that converges at the level of analyte detection and that provides readily comparable quantitative data across analytes. [0117] The kit is used on an individual showing signs of aging. The data indicates that certain aging related pathways, such as inflammation and telomere length, appear normal, while Ref. No. VDN.001WO SIRTUIN/TOR signaling appears defective. The individual adopts a caloric restriction diet that perturbs SIRTUIN/TOR signaling, and observes an alleviation in age-related symptoms. [0118] Example 6. Cancer stage characterization [0119] A patient is subjected to a routine cancer check and a tumor is detected. The tumor is subjected to standard, separated assays and is determined to have an oncogenic protein. [0120] The tumor is subjected to an assay through the systems disclosed herein and it is determined that the tumor cells exhibit a chromatin conformation consistent with pre- metastatic status, slight transcriptome aberrations and expression of the oncogenic protein at low levels. [0121] The tumor is determine to be early stage and non-metastatic, and is treated by a localized intervention rather than through a much more traumatic systemic therapeutic regimen. [0122] Example 7. Chemotherapy efficacy monitoring. [0123] A patient is found to have cancer warranting chemotherapeutic intervention. An assay as disclosed herein is performed and the patient is found to have transcripts and proteins indicative of metastasis, and to have chromatin configurations consistent with advanced cancer. [0124] The patient undergoes chemotherapy to clear the cancer cells. Ongoing monitoring indicates that the transcripts and proteins indicative of metastasis steadily decline concurrently with treatment. [0125] The treatment regimen is completed. Monitoring indicates that transcripts and proteins indicative of metastasis have returned to healthy levels, and the patient ceases to exhibit symptoms of cancer warranting intervention. [0126] Monitoring also indicates that the patient still exhibits chromatin configurations consistent with advanced cancer. A follow-up treatment is selected to target tumor cells not cleared by the chemotherapy treatment regimen, and the cancer is cleared.

Claims

Ref. No. VDN.001WO CLAIMS What is claimed is as follows: 1. A method comprising generating a circular nucleic acid indicative of an analyte in a sample; annealing the circular nucleic acid to a surface oligo of a microparticle comprising a plurality of surface oligos; contacting the circular nucleic acid to a polymerase, dNTPs and a buffer consistent with nucleic acid extension; extending the surface oligo to form a concatemer of the circular nucleic acid tethered to the microparticle; depositing the microparticle in a well of a microarray; contacting the microarray to a first probe; and assaying for a signal indicative of the first probe bound to the concatemer. 2. The method of claim 1, wherein generating the circular nucleic acid indicative of an analyte in a sample comprises annealing a linear precursor nucleic acid to a guide such that the 5’ end and 3’ end of the linear precursor are held in proximity, and ligating the 5’ and 3’ ends of the linear precursor. 3. The method of claim 2, wherein the guide comprises a nucleic acid in the sample. 4. The method of claim 2, wherein the guide comprises a nucleic acid that tags an antibody targeting an analyte in the sample. 5. The method of claim 2, wherein the guide comprises a PCR amplicon from the sample. 6. The method of claim 2, wherein the guide comprises an RNA molecule transcribed from a promoter-tagged fragment of the sample. 7. The method of claim 2, wherein the guide is generated by tagmentation. 8. The method of claim 2, wherein the guide is generated by revers-transcription. 9. The method of claim 2, wherein the guide is generated by cleaving a nucleic acid of the sample. 10. The method of claim 2, wherein the guide is generated by attaching primer binding sites at ends of a nucleic acid fragment of the sample. 11. The method of claim 2, wherein the guide is generated by attaching transcription promoter sites ad at least one end of a nucleic acid fragment of the sample. 12. The method of claim 2, wherein the guide comprises an oligo tag attached to an analyte binding moiety. 13. The method of claim 13, wherein the analyte binding moiety comprises an antibody binding domain. 14. The method of claim 13, wherein the analyte binding moiety comprises an antibody. Ref. No. VDN.001WO 15. The method of claim 13, wherein the analyte binding moiety comprises a receptor. 16. The method of claim 13, wherein the analyte binding moiety comprises a ligand. 17. The method of claim 13, wherein the analyte binding moiety comprises an aptamer. 18. The method of claim 4, wherein the analyte is a protein. 19. The method of claim 1, wherein the circular nucleic acid comprises a segment indicative of the analyte in the sample. 20. The method of claim 1, wherein the circular nucleic acid comprises a segment indicative of the sample. 21. The method of claim 1, wherein the surface oligo is covalently bound to the microparticle. 22. The method of claim 1, wherein contacting the circular nucleic acid to a polymerase comprises washing the microparticle. 23. The method of claim 1, wherein extending the surface oligo to form a concatemer of the circular nucleic acid tethered to the microparticle is performed under isothermal conditions. 24. The method of claim 23, wherein said isothermal conditions comprise room temperature extension. 25. The method of claim 23, wherein said isothermal conditions comprise extension at about 70 degrees C. 26. The method of claim 1, wherein the depositing occurs subsequent to the extending. 27. The method of claim 1, wherein the depositing occurs prior to the extending. 28. The method of claim 1, wherein the microarray comprises at least 100 wells. 29. The method of claim 1, wherein the microarray comprises at least 1000 wells. 30. The method of claim 1, wherein the microarray comprises at least 10,000 wells. 31. The method of claim 1, wherein the microarray exhibits at least 90% well occupancy. 32. The method of claim 1, wherein the microarray exhibits at least 95% well occupancy. 33. The method of claim 1, wherein the microarray exhibits at least 99% well occupancy. 34. The method of claim 1, wherein assaying for a signal indicative of the first probe bound to the concatemer comprises capturing an image of the array. 35. The method of claim 34, wherein capturing the image comprises using a portable device. 36. The method of claim 34, wherein capturing the image comprises using an optics system coupled to the array. Ref. No. VDN.001WO 37. The method of claim 1, comprising removing the first probe and contacting the microarray to a second probe, and assaying for a signal indicative of the second probe bound to the concatemer. 38. The method of claim 1, wherein the method detects an analyte in the sample. 39. The method of claim 1, wherein the method quantified an analyte in the sample. 40. The method of claim 1, wherein the method detects at least 100 distinct analytes in the sample. 41. The method of claim 1, wherein the method quantifies at least 100 distinct analytes in the sample. 42. The method of claim 1, wherein the method detects at least 1000 distinct analytes in the sample. 43. The method of claim 1, wherein the method quantifies at least 1000 distinct analytes in the sample. 44. The method of claim 1, wherein the method detects at least 10,000 distinct analytes in the sample. 45. The method of claim 1, wherein the method quantifies at least 10,000 distinct analytes in the sample. 46. The method of claim 1, wherein the method is practiced on an individual at two distinct time points. 47. The method of claim 46, wherein a treatment is administered to the patient between the two distinct time points. 48. The method of claim 46, wherein a treatment is administered to the patient prior to the two distinct time points. 49. The method of claim 46, wherein a treatment is administered to the patient concurrently with at least one of the two distinct time points. 50. A system comprising components for execution of the method of claim 1. 51. The system of claim 50, configured to analyze a plurality of analytes. 52. The system of claim 50, configured to analyze a plurality of analyte types. 53. The system of claim 50, configured to analyze a nucleic acid analyte and a polypeptide analyte. 54. The system of claim 50, configured to analyze a chromatin status. 55. A kit comprising reagents for operation of the system of claim 50. 56. A composition comprising a first microparticle having a surface coating of oligos, at least one of which is bound to a first circular nucleic acid. Ref. No. VDN.001WO 57. The composition of claim 56, wherein the first microparticle is deposited in a well. 58. The composition of claim 57, wherein the well is a constituent of a patterned array of at least 100 wells. 59. The composition of claim 57, wherein the well is a constituent of a patterned array of at least 1,000 wells. 60. The composition of claim 57, wherein the well is a constituent of a patterned array of at least 10,000 wells. 61. The composition of claim 57, wherein the well is a constituent of a patterned array that exhibits at least 90% well occupancy. 62. The composition of claim 57, wherein the well is a constituent of a patterned array that exhibits at least 95% well occupancy. 63. The composition of claim 57, wherein the well is a constituent of a patterned array that exhibits at least 99% well occupancy. 64. The composition of claim 56, further comprising a polymerase, dNTPs, and a buffer suitable for nucleic acid extension. 65. The composition of claim 56, further comprising a second microparticle bound to a second circular nucleic acid. 66. The composition of claim 65, wherein the first circular nucleic acid corresponds to a first target analyte and the second circular nucleic acid corresponds to a second target analyte. 67. The composition of claim 66, wherein the first target analyte is a nucleic acid. 68. The composition of claim 67, wherein the nucleic acid has a sequence corresponding to an expressed RNA molecule. 69. The composition of claim 67, wherein the nucleic acid has a sequence corresponding to an exposed chromosomal segment of chromatin. 70. he composition of claim 67, wherein the nucleic acid has a sequence corresponding to a cancer cell transcriptome transcript. 71. The composition of claim 67, wherein the nucleic acid has a sequence corresponding to a transcript differentially expressed in response to a cell treatment. 72. The composition of claim 67, wherein the nucleic acid has a sequence corresponding to a transcript differentially expressed in a cell cycle. 73. The composition of claim 67, wherein the nucleic acid has a sequence corresponding to a transcript differentially expressed in response to a disease. 74. The composition of claim 67, wherein the nucleic acid has a sequence corresponding to a transcript differentially expressed in a specific tissue. Ref. No. VDN.001WO 75. The composition of claim 67, wherein the second target analyte is a protein. 76. The composition of claim 66, wherein the first target analyte is a protein. 77. The composition of claim 56, wherein the first circular nucleic acid comprises a sample barcode. 78. The composition of claim 56, wherein the first circular nucleic acid comprises a segment indicative of a target analyte. 79. The composition of claim 56, wherein the first circular nucleic acid comprises a segment that anneals to a target analyte. 80. The composition of claim 56, wherein the bound oligo is subjected to a polymerase extension reaction to form a concatemer of the circular nucleic acid. 81. A microparticle comprising a plurality of covalently bound surface oligos, at least one of which shares a common phosphodiester backbone with a concatemeric repeat of a circular nucleic acid molecule. 82. The microparticle of claim 81, wherein the microparticle is deposited in a microarray well of a microarray. 83. The microparticle of claim 82, wherein the microarray comprises at least 100 wells. 84. The microparticle of claim 82, wherein the microarray comprises at least 1000 wells. 85. The microparticle of claim 82, wherein the microarray comprises at least 10,000 wells. 86. The microparticle of claim 82, wherein the microarray exhibits at least 90% well occupancy. 87. The microparticle of claim 82, wherein the microarray exhibits at least 95% well occupancy. 88. The microparticle of claim 82, wherein the microarray exhibits at least 99% well occupancy. 89. The microparticle of claim 81, comprising a probe bound to a repeating segment of the concatemeric repeat. 90. The microparticle of claim 89, wherein the probe comprises a fluorophore. 91. The microparticle of claim 89, wherein the repeating segment comprises a sample identifying sequence. 92. The microparticle of claim 89, wherein the repeating segment comprises a target analyte identifying sequence. 93. The microparticle of claim 89, wherein the repeating segment comprises a target analyte sequence. Ref. No. VDN.001WO 94. The microparticle of claim 89, wherein the repeating segment comprises a microparticle surface oligo binding sequence. 95. An array comprising a plurality of wells, at least some of the wells each harboring no more than one nanoparticle per well, wherein the nanoparticles comprise covalently surface bound oligos, and wherein at least a portion of the nanoparticles are bound to circular reporter nucleic acids. 96. The array of claim 95, wherein the circular reporter nucleic acids comprise circular reporter nucleic acids corresponding to target nucleic acids. 97. The array of claim 95, wherein the circular reporter nucleic acids comprise circular reporter nucleic acids corresponding to tags indicative of target analytes. 98. The array of claim 95, wherein the circular reporter nucleic acids comprise a first population of circular reporter nucleic acids corresponding to target analyte nucleic acids and a second population of circular reporter nucleic acids corresponding to target analyte polypeptides. 99. The array of claim 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from a single sample. 100. The array of claim 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least two samples. 101. The array of claim 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least 10 samples. 102. The array of claim 98, wherein the circular reporter nucleic acids correspond to target analytes and target nucleic acids from at least 100 samples. 103. The array of claim 95, wherein the circular reporter nucleic acids comprise sample barcodes. 104. The array of claim 97, wherein the circular reporter nucleic acids comprises target analyte identifying barcodes. 105. The array of claim 98, wherein the circular reporter nucleic acids comprises target analyte identifying barcodes. 106. The array of any one of claims 95 - 105, wherein the circular reporter nucleic acids are tethered to the at least a portion of the nanoparticles through the surface bound oligos. 107. The array of any one of claims 95 - 105, wherein at least some of the surface oligos are extended to comprise concatemeric repeats of circular reporter nucleic acids. 108. The array of claim 95, wherein at least some of the surface oligos are extended to comprise concatemeric repeats of circular reporter nucleic acids. Ref. No. VDN.001WO 109. The array of claim 108, comprising a first population of probes bound to the concatemeric repeats of the circular nucleic acids. 110. The array of claim 95, wherein at least some of the plurality of wells are occupied. 111. The array of claim 95, wherein at least 90% of the plurality of wells are occupied. 112. The array of claim 95, wherein at least 95% of the plurality of wells are occupied. 113. The array of claim 95, wherein at least 99% of the plurality of wells are occupied. 114. A dataset comprising data generated through the method of claim 1, wherein the dataset comprises nucleic acid data, polypeptide data. 115. The dataset of claim 114, wherein the dataset comprises analyte data for at least 100 analytes. 116. The dataset of claim 114, wherein the dataset comprises analyte data for at least 200 analytes. 117. The dataset of claim 114, wherein the dataset is generated in no more than 4 hours. 118. The dataset of claim 114, wherein the dataset is generated in no more than 1 hour.
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