Granted Patent
B2
US 12,421,541 · App. 19/048,060 · Granted Sep 23, 2025
Multiomic analysis device and methods of use thereof
Inventors:
Sandor Kovacs (Encinitas, CA); Eli N. Glezer (Del Mar, CA); Christopher Frye (San Diego, CA)
Assignee:
Singular Genomics Systems, Inc.
View Patent ↗
Loading inventors, assignments & file history…
Abstract
Disclosed herein, inter alia, are devices, compositions, kits, and methods for interrogating biological samples.
Claims (22)
1. A method of detecting polynucleotides with a microfluidic device, said method comprising:
positioning a first solid support in the microfluidic device, wherein the first solid support comprises a plurality of immobilized oligonucleotides, contacting the first solid support with a plurality of target nucleic acid molecules, amplifying the target nucleic acid molecules to generate a plurality of first amplification products immobilized to the first solid support, and sequencing the first amplification products; and
positioning a second solid support in the microfluidic device, wherein the second solid support comprises a tissue or cell, contacting a second solid support with a plurality of polynucleotide probes, amplifying the polynucleotide probes to generate a plurality of second amplification products in the cell or tissue, and sequencing the second amplification products.
2. The method of claim 1 , wherein sequencing comprises detecting a sequence of fluorescent signals.
3. The method of claim 1 , wherein sequencing comprises sequencing-by-synthesis, sequencing by ligation, sequencing-by-hybridization, or pyrosequencing, and sequencing generates a sequencing read.
4. The method of claim 1 , further comprising contacting the second solid support with eosin and/or 4′, 6-diamidino-2-phenylindole (DAPI) sand detecting the eosin or DAPI.
5. The method of claim 1 , wherein the second solid support comprises a tissue, wherein the tissue is about 5 μm to about 12 μm.
6. The method of claim 1 , wherein the first solid support comprises 2 to 12 fluidic channels and wherein the second solid support comprises 2 to 12 fluidic channels.
7. The method of claim 1 , wherein the immobilized oligonucleotides are covalently attached to a polymer, and the polymer is attached to the solid support.
8. The method of claim 1 , wherein the polynucleotide probes comprise a barcode sequence.
9. The method of claim 1 , wherein a polynucleotide probe binds to an RNA molecule.
10. The method of claim 1 , wherein a polynucleotide probe binds to an oligonucleotide attached to a protein.
11. The method of claim 1 , wherein a polynucleotide probe binds to an oligonucleotide attached to a cellular component.
12. The method of claim 1 , wherein the first solid support comprises glass, and the second solid support comprises glass.
13. The method of claim 1 , wherein the second solid support comprises a plurality of discrete regions, wherein each discrete region comprises a plurality of cells, wherein each discrete region is each other by about 1 mm to 5 mm.
14. The method of claim 13 , wherein the second solid support comprises a coating for enhanced cell adhesion.
15. The method of claim 1 , wherein sequencing the second amplification products occurs after sequencing the first amplification products.
16. The method of claim 1 , amplifying the target nucleic acid molecules comprises bridge-PCR or rolling circle amplification.
17. The method of claim 1 , amplifying the target nucleic acid molecules comprises rolling circle amplification.
18. The method of claim 1 , wherein the second solid support is contacted with a plurality of polynucleotide probes, each polynucleotide probe comprising a different sequencing primer.
19. The method of claim 18 , wherein sequencing the amplification products comprises hybridizing a first sequencing primer to an amplification product comprising a first sequencing primer binding sequence, followed by hybridizing a second sequencing primer to an amplification product comprising a second sequencing primer binding sequence.
20. The method of claim 1 , wherein the second solid support comprises a plurality of discrete regions, wherein each discrete region comprises a plurality of tissues, wherein each discrete region is each other by about 1 mm to 5 mm.
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Aug 29, 2025
From: KOVACS, SANDOR; GLEZER, ELI N.; FRYE, CHRISTOPHER
To: SINGULAR GENOMICS SYSTEMS, INC.
Reel/Frame 072127/0594 →
Continuity (4)
Continuation
PCTUS2022027630
· May 4, 2022
Provisional Application
63184684
· May 5, 2021
References Cited (320)
US 4318846A
· Khanna et al.
· 1982
[cited by applicant]
US 4792520A
· Stambrook et al.
· 1988
[cited by applicant]
US 5034506A
· Summerton et al.
· 1991
[cited by applicant]
US 5066580A
· Lee
· 1991
[cited by applicant]
US 5188934A
· Menchen et al.
· 1993
[cited by applicant]
US 5235033A
· Summerton et al.
· 1993
[cited by applicant]
US 5366860A
· Bergot et al.
· 1994
[cited by applicant]
US 5538724A
· Butcher et al.
· 1996
[cited by applicant]
US 5599675A
· Brenner et al.
· 1997
[cited by applicant]
US 5688648A
· Mathies et al.
· 1997
[cited by applicant]
US 5750341A
· Macevicz
· 1998
[cited by applicant]
US 5763594A
· Hiatt et al.
· 1998
[cited by applicant]
US 5800996A
· Lee et al.
· 1998
[cited by applicant]
US 5808045A
· Hiatt et al.
· 1998
[cited by applicant]
US 5847162A
· Lee et al.
· 1998
[cited by applicant]
US 5872244A
· Hiatt et al.
· 1999
[cited by applicant]
US 6210891B1
· Nyren et al.
· 2001
[cited by applicant]
US 6218122B1
· Friend et al.
· 2001
[cited by applicant]
US 6232465B1
· Hiatt et al.
· 2001
[cited by applicant]
US 6258568B1
· Nyren
· 2001
[cited by applicant]
US 6271022B1
· Bochner
· 2001
[cited by applicant]
US 6274320B1
· Rothberg et al.
· 2001
[cited by applicant]
US 6365367B1
· Friedman et al.
· 2002
[cited by applicant]
US 6664079B2
· Ju et al.
· 2003
[cited by applicant]
US 7057026B2
· Barnes et al.
· 2006
[cited by applicant]
US 7264929B2
· Rothberg et al.
· 2007
[cited by applicant]
US 7271952B2
· Suzuki et al.
· 2007
[cited by applicant]
US 7390463B2
· He et al.
· 2008
[cited by applicant]
US 7541444B2
· Milton et al.
· 2009
[cited by applicant]
US 8003354B2
· Shen et al.
· 2011
[cited by applicant]
US 8039817B2
· Feng et al.
· 2011
[cited by applicant]
US 8178360B2
· Barnes et al.
· 2012
[cited by applicant]
US 8241573B2
· Banerjee et al.
· 2012
[cited by applicant]
US 8551710B2
· Bernitz et al.
· 2013
[cited by applicant]
US 9371598B2
· Chee
· 2016
[cited by applicant]
US 9556473B2
· Bernitz et al.
· 2017
[cited by applicant]
US 9593365B2
· Frisen et al.
· 2017
[cited by applicant]
US 9598723B2
· Ammann et al.
· 2017
[cited by applicant]
US 20010054691A1
· Park et al.
· 2001
[cited by applicant]
US 20020159919A1
· Churchill et al.
· 2002
[cited by applicant]
US 20030032024A1
· Lizardi
· 2003
[cited by applicant]
US 20030082556A1
· Kaufman et al.
· 2003
[cited by applicant]
US 20030143536A1
· Lizardi
· 2003
[cited by applicant]
US 20050089860A1
· Arita
· 2005
[cited by applicant]
US 20050208644A1
· Takiguchi et al.
· 2005
[cited by applicant]
US 20060050376A1
· Houston et al.
· 2006
[cited by applicant]
US 20060292559A1
· Reddy et al.
· 2006
[cited by applicant]
US 20070077580A1
· Ikeda et al.
· 2007
[cited by applicant]
US 20090298718A1
· Denman et al.
· 2009
[cited by applicant]
US 20100055733A1
· Lutolf et al.
· 2010
[cited by applicant]
US 20110059865A1
· Smith et al.
· 2011
[cited by applicant]
US 20110223585A1
· Gullberg et al.
· 2011
[cited by applicant]
US 20120301886A1
· Farrell et al.
· 2012
[cited by applicant]
US 20140056811A1
· Jacob et al.
· 2014
[cited by applicant]
US 20140057799A1
· Johnson et al.
· 2014
[cited by applicant]
US 20160257993A1
· Fu et al.
· 2016
[cited by applicant]
US 20160369329A1
· Cai et al.
· 2016
[cited by applicant]
US 20170107563A1
· Samusik et al.
· 2017
[cited by applicant]
US 20190017106A1
· Frisen et al.
· 2019
[cited by applicant]
US 20190071668A1
· Schmidt et al.
· 2019
[cited by applicant]
US 20190113423A1
· Goodman et al.
· 2019
[cited by applicant]
US 20190155835A1
· Daugharthy et al.
· 2019
[cited by applicant]
US 20190376123A1
· Bobrow et al.
· 2019
[cited by applicant]
US 20200277663A1
· Iyer et al.
· 2020
[cited by applicant]
US 20200277664A1
· Frenz
· 2020
[cited by applicant]
US 20200362334A1
· Regev et al.
· 2020
[cited by applicant]
US 20210039062A1
· Mirkin et al.
· 2021
[cited by applicant]
US 20210108195A1
· Bernate et al.
· 2021
[cited by applicant]
US 20210238662A1
· Bava et al.
· 2021
[cited by applicant]
US 20210382033A1
· Mir
· 2021
[cited by applicant]
US 20210388424A1
· Bava
· 2021
[cited by applicant]
US 20220229044A1
· Feldman et al.
· 2022
[cited by applicant]
US 20230088043A1
· Kovacs et al.
· 2023
[cited by applicant]
US 20230100215A1
· Glezer et al.
· 2023
[cited by applicant]
JP 2005265627A
· 2005
[cited by applicant]
JP 5970959B2
· 2016
[cited by applicant]
WO 8910977A1
· 1989
[cited by applicant]
WO 9607669A1
· 1996
[cited by applicant]
WO 2004018497A2
· 2004
[cited by applicant]
WO 2004018497A3
· 2004
[cited by applicant]
WO 2005039389A2
· 2005
[cited by applicant]
WO 2008042067A2
· 2008
[cited by applicant]
WO 2012106385A2
· 2012
[cited by applicant]
WO 2013090360A2
· 2013
[cited by applicant]
WO 2013090360A3
· 2013
[cited by applicant]
WO 2014030066A2
· 2014
[cited by applicant]
WO 2014030066A3
· 2014
[cited by applicant]
WO 2017079382A1
· 2017
[cited by applicant]
WO 2018091676A1
· 2018
[cited by applicant]
WO 2018148723A1
· 2018
[cited by applicant]
WO 2019068880A1
· 2019
[cited by applicant]
WO 2019084062A1
· 2019
[cited by applicant]
WO 2019199579A1
· 2019
[cited by applicant]
WO 2019222284A1
· 2019
[cited by applicant]
WO 2020028194A1
· 2020
[cited by applicant]
WO 2020056044A1
· 2020
[cited by applicant]
WO 2020076976A1
· 2020
[cited by applicant]
WO 2020076979A1
· 2020
[cited by applicant]
WO 2020096687A1
· 2020
[cited by applicant]
WO 2020099640A1
· 2020
[cited by applicant]
WO 2020123309A1
· 2020
[cited by applicant]
WO 2020160044A1
· 2020
[cited by applicant]
WO 2022056385A1
· 2022
[cited by applicant]
WO 2022235764A1
· 2022
[cited by applicant]
International Search Report and Written Opinion issued in International Application No. PCT/US2021/045104, Nov. 23, 2021, 15 pages.
[cited by applicant]
International Search Report and Written Opinion issued in International Application No. PCT/US2021/045105, Jan. 31, 2022, 18 pages.
[cited by applicant]
International Search Report and Written Opinion issued in International Application No. PCT/US2022/027630, Sep. 19, 2022, 14 pages.
[cited by applicant]
(2023) Researchers Fully Sequence the Y Chromosome for the First Time, National Institute of Standards and Technology, pp. 1-4.
[cited by applicant]
(2006) The Cancer Genome Atlas Program (TCGA), National Cancer Institute Center for Cancer Genomics, www.cancer.gov/tcga, 2 pages.
[cited by applicant]
(1988) The Stratagene Catalog, pp. 39.
[cited by applicant]
Agrawal et al., (Nov. 15, 2016) “Nivolumab dose selection: challenges, opportunities, and lessons learned for cancer immunotherapy”, Journal of Immunotherapy Cancer, 4:72 (11 pages).
[cited by applicant]
Ahern H, (1995) “Biochemical, reagent kits offer scientists good return on investment”, The Scientist, 9(15):20.
[cited by applicant]
Alon et al., (2021) “Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems”, Science, 371(6528): eaax2656.
[cited by applicant]
ANSI, (Jan. 9, 2004) “ANSI SLAS Jan. 2004 (R2012): for Microplates—Footprint Dimensions”, Secretariat Society for Laboratory Automation and Screening, 8 pages.
[cited by applicant]
ANSI, (Jan. 9, 2004) “ANSI SLAS Feb. 2004 (R2012): for Microplates—Height Dimensions”, Secretariat Society for Laboratory Automation and Screening, 9 pages.
[cited by applicant]
ANSI, (Jan. 9, 2004) “ANSI SLAS Mar. 2004 (R2012): for Microplates—Bottom Outside Flange Dimensions”, Secretariat Society for Laboratory Automation and Screening, 10 pages.
[cited by applicant]
ANSI, (Jan. 9, 2004) “ANSI SLAS Apr. 2004 (R2012): for Microplates—Well Positions”, Secretariat Society for Laboratory Automation and Screening, 13 pages.
[cited by applicant]
ANSI, (Apr. 9, 2009) “ANSI SLAS Jun. 2012: for Microplates—Well Bottom Elevation”, Secretariat Society for Laboratory Automation and Screening, 9 pages.
[cited by applicant]
Arce et al., (Jul. 24, 2013) “Fast and Accurate Automated Cell Boundary Determination for Fluorescence Microscopy”, Scientific Reports, 3(1):2266 (1-6).
[cited by applicant]
Auld et al., (Jun. 1, 2020) “Microplate Selection and Recommended Practices in High-throughput Screening and Quantitative Biology”, Assay Guidance Manual [Internet], 50 pages.
[cited by applicant]
Bains et al., (Dec. 7, 1988) “A Novel Method For Nucleic Acid Sequence Determination”, Journal of Theoretical Biology, 135(3):303-307.
[cited by applicant]
Bains et al., (May 28, 2009) “Quantifying The Development of the Peripheral Naive CD4+ T-cell Pool in Humans”, Blood, 113(22):5480-5487.
[cited by applicant]
Bullinger et al., (2004) “Use Of Gene-Expression Profiling To Identify Prognostic Subclasses In Adult Acute Myeloid Leukemia”, New England Journal of Medicine, 350(16):1605-1616.
[cited by applicant]
Cai Matthew, (2019) “Spatial Mapping of Single Cells in Human Cerebral Cortex Using Dartfish: a Highly Multiplexed Method for in Situ Quantification of Targeted RNA Transcripts”, University of California, San Diego, 107…
[cited by applicant]
Carow et al., (2019) “Spatial And Temporal Localization Of Immune Transcripts Defines Hallmarks and Diversity in the Tuberculosis Granuloma”, Nature Communications, 10(1):1823 (15 pages).
[cited by applicant]
Carpenter et al., (Oct. 31, 2006) “Cellprofiler: Image Analysis Software for Identifying and Quantifying Cell Phenotypes”, Genome Biology, 7(10):R100 (11 pages).
[cited by applicant]
Catuogno et al., (2011) “Recent Advance in Biosensors for MicroRNAs Detection in Cancer”, Cancers, 3(2):1877-1898.
[cited by applicant]
Chen et al., (2018) “Efficient in Situ Barcode Sequencing Using Padlock Probe-based BaristaSeq”, Nucleic Acids Research, 46(4):Article e22 (pp. 1-10).
[cited by applicant]
Chen et al., (Jan. 30, 2015) “Optical imaging. Expansion Microscopy”, Science, 347(6221):543-548 (13 pages).
[cited by applicant]
Chen et al., (2015) “RNA Imaging. Spatially Resolved, Highly Multiplexed RNA Profiling in Single Cells”, Science, 348(6233) :aaa6090.
[cited by applicant]
Christian et al., (Dec. 4, 2001) “Detection of DNA Point Mutations and mRNA Expression Levels By Rolling Circle Amplification in Individual Cells”, PNAS USA, 98(25):14238-14243.
[cited by applicant]
Daigeler et al., (2006) “Clinicopathological Findings In A Case Series Of Extrathoracic Solitary Fibrous Tumors of Soft Tissues”, BMC surgery, 6:1-8.
[cited by applicant]
Basiji David, (Apr. 1, 2007) “Multispectral Imaging Flow Cytometry”, Biomedical Imaging: From Nano To Macro, 1100-1103.
[cited by applicant]
Denkert et al., (2015) “Strategies For Developing Ki67 As A Useful Biomarker In Breast Cancer”, The Breast, 24:S67-S72.
[cited by applicant]
Dirks et al., (2004) “Triggered Amplification By Hybridization Chain Reaction”, Proceedings of the National Academy of Sciences of the United States of America, 101(43):15275-15278.
[cited by applicant]
Drmanac et al., (Jan. 1998) “Accurate Sequencing by Hybridization For DNA Diagnostics and Individual Genomics”, Nature Biotechnology, 16(1):54-58.
[cited by applicant]
Edelman et al., (1997) “The Utility of Follow-up Testing After Curative Cancer Therapy: A Critical Review and Economic Analysis”, JGIM, 12(5):318-331.
[cited by applicant]
El-Sagheer et al., (Mar. 22, 2012) “Click Nucleic Acid Ligation: Applications in Biology and Nanotechnology”, Accounts of Chemical Research, 45(8):1258-1267.
[cited by applicant]
Fan et al., (2018) “Branched Rolling Circle Amplification Method for Measuring Serum Circulating MicroRNA Levels for Early Breast Cancer Detection”, Cancer Science, 109(9):2897-2906.
[cited by applicant]
Feeney et al., (Apr. 1, 1982) “Chemical Modification of Proteins: An Overview”, Advances in Chemistry Series, 198:3-55.
[cited by applicant]
Fijnvandraat et al., (2002) “Non-Radioactive In Situ Detection of mRNA in ES CellDerived Cardiomyocytes and in the Developing Heart”, Microscopy Research and Techniques, 58:387-394.
[cited by applicant]
Fodor et al., (Feb. 15, 1991) “Light-Directed, Spatially Addressable Parallel Chemical Synthesis”, Science, 251(4995):767-773.
[cited by applicant]
Fredriksson et al., (2007) “Multiplexed protein detection by proximity ligation for cancer biomarker validation”, Nature methods, 4(4):327-329.
[cited by applicant]
Fredriksson et al., (2002) “Protein Detection Using Proximity-Dependent DNA Ligation Assays”, Nature biotechnology, 20(5):473-477.
[cited by applicant]
Ganusov et al., (Dec. 2007) “Do Most Lymphocytes in Humans Really Reside in the Gut?”, Trends Immunology, 28(12):514-518.
[cited by applicant]
Gao et al., (Dec. 2019) “Rolling circle Amplification for Single Cell Analysis and in situ Sequencing”, Trends in Analytical Chemistry, vol. 121:115700 (7 pages).
[cited by applicant]
Gelali et al., (Apr. 9, 2019) “iFISH is a Publically Available Resource Enabling Versatile Dna Fish to Study Genome Architecture”, Nature communications, 10(1):1636 (15 pages).
[cited by applicant]
Gore et al., (Mar. 3, 2011) “Somatic Coding Mutations in Human Induced Pluripotent Stem Cells”, Nature, 471(7336):63-67 (14 pages).
[cited by applicant]
Gullberg et al., (Jun. 1, 2004) “Cytokine Detection By Antibody-Based Proximity Ligation”, PNAS, 101 (22): 8420-8424.
[cited by applicant]
Guo et al., (Jul. 8, 2008) “Four-Color DNA Sequencing With 3′—O—Modified Nucleotide Reversible Terminators and Chemically Cleavable Fluorescent Dideoxynucleotides”, Proceedings of the National Academy of Sciences of the…
[cited by applicant]
Gyllborg et al., (2020) “Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue”, Nucleic Acids Research, 48(19):e112.
[cited by applicant]
Hagai et al., (Oct. 24, 2018) “Gene Expression Variability Across Cells and Species Shapes Innate Immunity”, Nature, 563(7730):197-202.
[cited by applicant]
Hamady et al., (Mar. 2008) “Error-Correcting Barcoded Primers for Pyrosequencing Hundreds of Samples in Multiplex”, Nature Methods, 5(3):235-237.
[cited by applicant]
Hamilton Nicholas, (Aug. 2009) “Quantification and its Applications in Fluorescent Microscopy Imaging”, Traffic, 10(8):951-961.
[cited by applicant]
Hardenbol et al., (2003) “Multiplexed Genotyping with Sequence-Tagged Molecular Inversion Probes”, Nature Biotechnology, 21(6):673-678.
[cited by applicant]
Heintzmann et al., (2017) “Super-Resolution Structured Illumination Microscopy”, Chemical Reviews, 117(23):13890-13908.
[cited by applicant]
Hu et al., (2014) “Sensitive Quantification of Messenger RNA with a Real-Time Ligase Chain Reaction by Using a Ribonucleotide-Modified DNA Probe”, Chemical Communications, 50(86):13093-13095.
[cited by applicant]
Jeong et al., (2020) “Current Immunoassay Methods and Their Applications to Clinically Used Biomarkers of Breast Cancer”, Clinical Biochemistry, 78:43-57.
[cited by applicant]
Kappler et al., (Aug. 2020) “Emergence and Significance of Carbohydrate-specific Antibodies”, Genes & Immunity, 21(4):224-239.
[cited by applicant]
Kato et al., (Feb. 1, 1995) “Polymerization of Methyl Methacrylate with the Carbon Tetrachloride/Dichlorotris (triphenylphosphine)ruthenium(II)/Methylaluminum Bis(2,6-di-tert-butylphenoxide) Initiating System: Possibili…
[cited by applicant]
Ke et al., (2013) “In Situ Sequencing for RNA Analysis in Preserved Tissue and Cells”, Nature methods, 10(9):857-860.
[cited by applicant]
Klein et al., (Jul. 25, 2017) “InDrops and Drop-seq Technologies for Single-cell Sequencing”, Lab on a Chip, 17(15):2540-2541.
[cited by applicant]
Kobori et al., (2014) “Expanding possibilities of rolling circle amplification as a biosensing platform”, Analytical Sciences, 30(1):59-64.
[cited by applicant]
Krzywkowski et al., (2019) “Chimeric Padlock and llock Probes for Increased Efficiency of Targeted RNA Detection”, RNA, 25(1):82-89.
[cited by applicant]
Lage et al., (Feb. 2003) “Whole Genome Analysis Of Genetic Alterations In Small DNA Samples Using Hyperbranched Strand Displacement Amplification And Array-CGH”, Genome Research, 13(2):294-307.
[cited by applicant]
Lareau et al., (Feb. 13, 2020) “Inference and Effects of Barcode Multiplets in Droplet-based Single-cell Assays”, Nature Communications, 11(1):866 (1-9).
[cited by applicant]
Larsson et al., (Apr. 11, 2010) “In Situ Detection and Genotyping of Individual mRNA Molecules”, Nature methods, 7(5):395-397.
[cited by applicant]
Lee et al., (Mar. 2015) “Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues”, Nature Protocols, 10(3):442-458.
[cited by applicant]
Lee et al., (2014) “Highly multiplexed subcellular RNA sequencing in situ”, Science, 343(6177):1360-1363.
[cited by applicant]
Li et al., (May 29, 2009) “Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing”, Science, 324(5931): 1210-1213 (5 pages).
[cited by applicant]
Li et al., (Jun. 12, 2009) “Multiplex Padlock Targeted Sequencing Reveals Human Hypermutable CpG Variations”, Genome research, 19(9):1606-1615.
[cited by applicant]
Li et al., (2009) “Stand-Alone Rolling Circle Amplification Combined with Capillary Electrophoresis for Specific Detection of Small RNA”, Analytical Chemistry, 81:4906-4913.
[cited by applicant]
Lizardi et al., (Jul. 1998) “Mutation Detection and Single-Molecule Counting Using Isothermal Rolling-Circle Amplification”, Nature Genetics, 19(3):225-232.
[cited by applicant]
Lohmann et al., (2007) “Detection of short repeated genomic sequences on metaphase chromosomes using padlock probes and target primed rolling circle DNA synthesis”, BMC molecular biology, 8:103 (8 pages).
[cited by applicant]
Lubeck et al., (2014) “Single-cell in Situ RNA Profiling by Sequential Hybridization”, Nature Methods, 11(4):360-361.
[cited by applicant]
Lubeck et al., (2012) “Single-cell Systems Biology by Super-resolution Imaging and Combinatorial Labeling”, Nature Methods, 9(7):743-748.
[cited by applicant]
Lugagne et al., (Jul. 30, 2018) “Identification of Individual Cells from z-stacks of Bright-field Microscopy Images”, Scientific Reports, 8:11455 (5 pages).
[cited by applicant]
Lundin et al., (2020) “Spatiotemporal Mapping of RNA Editing in the Developing Mouse Brain Using in Situ Sequencing Reveals Regional and Cell-type-specific Regulation”, BMC Biology, 18(6):1-15.
[cited by applicant]
Mag et al., (Nov. 24, 1992) “Synthesis and Selective Cleavage of an Oligodeoxynucleotide Containing a Bridged Non-chiral Internucleotide 3′-phosphoramidate Linkage”, Tetrahedron Letters, 33(48):7319-7322.
[cited by applicant]
Magaki et al., (2019) “An Introduction To The Performance Of Immunohistochemistry”, Methods in Molecular Biology, 1897:289-298.
[cited by applicant]
Manoharan Vinothan N., (2010) “Digital Holographic Microscopy for 3D Imaging of Complex Fluids and Biological Systems National Academies of Sciences”, Engineering, and Medicine. 2010. Frontiers of Engineering: Reports o…
[cited by applicant]
Manuguerra et al., (May 1, 2018) “Gene Assembly via One-pot Chemical Ligation of DNA Promoted by DNA Nanostructures”, Chemical Communications, 54(36):4529-4532.
[cited by applicant]
Mignardi et al., (Apr. 2, 2014) “Fourth-Generation Sequencing in the Cell and the Clinic”, Genome Medicine, 6(31):1-4.
[cited by applicant]
Mirza et al., (Mar. 14, 2008) “Methods and Approaches for the Comprehensive Characterization and Quantification of Cellular Proteomes Using Mass Spectrometry”, Physiological Genomics, 33(1):3-11.
[cited by applicant]
Mitra et al., (2003) “Fluorescent In Situ Sequencing on Polymerase Colonies”, Analytical Biochemistry, 320:55-65.
[cited by applicant]
Moad et al., (Jun. 14, 2005) “Living Radical Polymerization by the RAFT Process”, Australian Journal of Chemistry, 58(6):379-410.
[cited by applicant]
Mohammadi-Kambs et al., (2017) “Hamming Distance as a Concept in DNA Molecular Recognition”, ACS Omega, 2(4):1302-1308.
[cited by applicant]
Nilsson et al., (Sep. 30, 1994) “Padlock Probes: Circularizing Oligonucleotides For Localized DNA Detection”, Science, 265(5181):2085-2088 (5 pages).
[cited by applicant]
Nitta et al., (2013) “New Methods for ALK Status Diagnosis in Non-Small-Cell Lung Cancer”, Journal of Thoracic Oncology, 8(8):1019-1031 (13 pages).
[cited by applicant]
Noggle et al., (Oct. 5, 2011) “Human Oocytes Reprogram Somatic Cells to a Pluripotent State”, Nature, 478(7367):70-75.
[cited by applicant]
Odeh et al., (Dec. 18, 2019) “Aptamers Chemistry: Chemical Modifications and Conjugation Strategies”, Molecules, 25(1):3 (51 pages).
[cited by applicant]
Otsu et al., (Feb. 16, 1982) “Role of initiator-transfer agent-terminator (iniferter) in radical polymerizations: Polymer design by organic disulfides as iniferters”, Macromolecular Rapid Communications, 3:127-132.
[cited by applicant]
Ouladan et al., (2015) “Differential diagnosis of solitary fibrous tumors: A study of 454 soft tissue tumors indicating the diagnostic value of nuclear State relocation and ALDH1 expression combined with in situ proximi…
[cited by applicant]
Park et al., (2013) “The role of chemotherapy in advanced solitary fibrous tumors: a retrospective analysis”, Clinical sarcoma research, 3(1):1-7.
[cited by applicant]
Patel et al., (Jun. 12, 2014) “Single-cell RNA-seq Highlights Intratumoral Heterogeneity in Primary Glioblastoma”, Science, 344(6190):1396-1401.
[cited by applicant]
Pattarone et al., (2021) “Learning Deep Features for Dead and Living Breast Cancer cell Classification without Staining”, Scientific Reports, 11:10304 (10 pages).
[cited by applicant]
Pearson et al., (May 13, 2016) “High-Level Clonal FGFR Amplification and Response to FGFR Inhibition in a Translational Clinical Trial”, Cancer Discovery, 6(8):838-851.
[cited by applicant]
Peerzade et al., (May 8, 2020) “Ultrabright Fluorescent Silica Nanoparticles for Multiplexed Detection”, Nanomaterials, 10(5):905 (14 pages).
[cited by applicant]
Peters et al., (Jan. 2011) “Multiparameter Flow Cytometry in the Diagnosis and Management of Acute Leukemia”, Archives of Pathology & Laboratory Medicine, 135(1):44-54.
[cited by applicant]
Porreca et al., (Nov. 2007) “Multiplex Amplification of Large Sets of Human Exons”, Nature Methods, 4(11):931-936.
[cited by applicant]
Ronaghi et al., (Jul. 17, 1998) “A Sequencing Method Based on Real-Time Pyrophosphate”, Science, 281(5375):363-365.
[cited by applicant]
Ronaghi et al., (Nov. 1, 1996) “Real-Time DNA Sequencing Using Detection of Pyrophosphate Release”, Analytical Biochemistry, 242(1):84-89.
[cited by applicant]
Ronaghi Mostafa, (2001) “Pyrosequencing Sheds Light on DNA Sequencing”, Genome Research, 11(1):3-11.
[cited by applicant]
Rouhanifard, (2018) “Exponential Fluorescent Amplification of Individual RNAs Using ClampFISH probes”, bioRxiv Preprint, Article 222794.
[cited by applicant]
Sansone et al., (Jun. 2019) “Spatial Transcriptomics Levels Up”, Nature Methods, 16(6):458 (1 page).
[cited by applicant]
Sapoznik et al., (2020) “A Versatile Oblique Plane Microscope for Large-scale and High-resolution Imaging of Subcellular Dynamics”, Cell Biology, 9:e57681 (39 pages).
[cited by applicant]
Schallmeiner et al., (2007) “Sensitive protein detection via triple-binder proximity ligation assays”, Nature methods, 4(2):135-137.
[cited by applicant]
Schlachter et al., (2009) “A Method to Unmix Multiple Fluorophores in Microscopy Images with Minimal a Priori Information”, Optics Express, 17(25):22747-22760.
[cited by applicant]
Shendure et al., (2005) “Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome”, Science, 309(5741):1728-1732.
[cited by applicant]
Shirawaka et al., (2004) “Blind Spectral Decomposition of Single-Cell Fluorescence by Parallel Factor Analysis”, Biophysical Journal, 86(3):1739-1752.
[cited by applicant]
Strell et al., (2019) “Placing RNA in Context and Space—Methods for Spatially Resolved Transcriptomics”, The FEBS Journal, 286(8): 1468-1481.
[cited by applicant]
Suzuki et al., (Dec. 20, 2019) “Characterization Of Cancer Omics And Drug Perturbations In Panels Of Lung Cancer Cells”, Sci. Rep, 9(1):19529 (15 pages).
[cited by applicant]
Takahashi et al., (2018) “RNase H-assisted RNA-Primed Rolling Circle Amplification for Targeted RNA Sequence Detection”, Scientific Reports, 8:7770 (11 pages).
[cited by applicant]
Tang et al., (2016) “Suppression of Rolling Circle Amplification by Nucleotide Analogs in Circular Template for Three DNA Polymerases”, Bioscience, biotechnology, and biochemistry, 80(8):1555-1561.
[cited by applicant]
Turczyk et al., (2020) “Spatial Sequencing: A Perspective”, Journal of biomolecular techniques: JBT, 31(2):44-46.
[cited by applicant]
Van Der Velden et al., (Jun. 2003) “Detection of minimal residual disease in hematologic malignancies by real-time quantitative PCR: principles, approaches, and laboratory aspects”, Leukemia, 17(6):1013-1034.
[cited by applicant]
Veregin et al., (Sep. 1, 1993) “Free radical polymerizations for narrow polydispersity resins: electron spin resonance studies of the kinetics and mechanism”, Macromolecules, 26(20):5316-5320.
[cited by applicant]
Vickovic et al., (Oct. 2019) “High-definition Spatial Transcriptomics for in Situ Tissue Profiling”, Nature Methods, 16(10):987-990 (14 pages).
[cited by applicant]
Walker et al., (Oct. 1, 1988) “Photolabile 1-(2-Nitrophenyl) Ethyl Phosphate Esters of Adenine Nucleotide Analogs. Synthesis and Mechanism of Photolysis”, Journal of the American Chemical Society, 110(21):7170-7177.
[cited by applicant]
Wang et al., (May 1, 1995) “Controlled/living radical polymerization. atom transfer radical polymerization in the presence of transition-metal complexes”, Macromolecules, 117(20):5614-5615.
[cited by applicant]
Wang et al., (Mar. 19, 2018) “Multiplexed Imaging of High-density Libraries of RNAs with Merfish and Expansion Microscopy”, Scientific Reports, 8(1):4847 (1-13).
[cited by applicant]
Wang et al., (Jul. 27, 2018) “Three-dimensional Intact-tissue Sequencing of Single-cell Transcriptional States”, Science, 361(6400):5691 (11 pages).
[cited by applicant]
Wassie et al., (2019) “Expansion Microscopy: Principles and Uses in Biological Research”, Nature methods, 16(1):33-41.
[cited by applicant]
Weibrecht et al., (2013) “In Situ Detection of Individual mRNA Molecules and Protein Complexes or Post-Translational Modifications Using Padlock Probes Combined with the In Situ Proximity Ligation Assay.”, Nature Protoc…
[cited by applicant]
Wilson et al., (Jul. 15, 2006) “Gene Expression Profiling of Adult Acute Myeloid Leukemia Identifies Novel Biologic Clusters for Risk Classification and Outcome Prediction”, Blood, 108(2):685-696.
[cited by applicant]
Xu et al., (2009) “Design of 240,000 Orthogonal 25mer DNA Barcode Probes”, PNAS, 106(7):2289-2294.
[cited by applicant]
Yaari et al., (Nov. 20, 2015) “Practical Guidelines For B-cell Receptor Repertoire Sequencing Analysis”, Genome Medicine, 7:121(14 pages).
[cited by applicant]
Yeole N., (May 25, 2010) “Thiocarbonylthio Compounds”, Synlett, 10:1572-1573.
[cited by applicant]
York et al., (Nov. 2013) “Instant super- Resolution Imaging in Live Cells and Embryos via Analog Image Processing”, Nature Methods, 10(11):1122-1126 (19 pages).
[cited by applicant]
Zhang et al., (Aug. 2009) “Digital RNA Allelotyping Reveals Tissue-specific and Allele- specific Gene Expression in Human”, Nature Methods, 6(8):613-618 (14 pages).
[cited by applicant]
Zheng et al., (Jan. 2017) “Massively Parallel Digital Transcriptional Profiling of Single Cells”, Nature Communications, 8:14049 (12 pages).
[cited by applicant]