Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-10-21

AUTHORS

Evgenij Fiskin, Caleb A. Lareau, Leif S. Ludwig, Gökcen Eraslan, Feimei Liu, Aaron M. Ring, Ramnik J. Xavier, Aviv Regev

ABSTRACT

Multimodal measurements of single-cell profiles are proving increasingly useful for characterizing cell states and regulatory mechanisms. In the present study, we developed PHAGE-ATAC (Assay for Transposase-Accessible Chromatin), a massively parallel droplet-based method that uses phage displaying, engineered, camelid single-domain antibodies (‘nanobodies’) for simultaneous single-cell measurements of protein levels and chromatin accessibility profiles, and mitochondrial DNA-based clonal tracing. We use PHAGE-ATAC for multimodal analysis in primary human immune cells, sample multiplexing, intracellular protein analysis and the detection of SARS-CoV-2 spike protein in human cell populations. Finally, we construct a synthetic high-complexity phage library for selection of antigen-specific nanobodies that bind cells of particular molecular profiles, opening an avenue for protein detection, cell characterization and screening with single-cell genomics. More... »

PAGES

374-381

References to SciGraph publications

  • 2011-03-09. Beyond natural antibodies: the power of in vitro display technologies in NATURE BIOTECHNOLOGY
  • 2020-12-18. Viral targets for vaccines against COVID-19 in NATURE REVIEWS IMMUNOLOGY
  • 2018-12-19. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics in GENOME BIOLOGY
  • 2021-06-03. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells in NATURE BIOTECHNOLOGY
  • 2020-05-04. Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes in NATURE METHODS
  • 2017-08-30. Multiplexed quantification of proteins and transcripts in single cells in NATURE BIOTECHNOLOGY
  • 2006-10-23. Targeting and tracing antigens in live cells with fluorescent nanobodies in NATURE METHODS
  • 2018-02-12. Yeast surface display platform for rapid discovery of conformationally selective nanobodies in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2017-07-31. Simultaneous epitope and transcriptome measurement in single cells in NATURE METHODS
  • 2019-06-24. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility in NATURE BIOTECHNOLOGY
  • 2005-09-01. Selecting and screening recombinant antibody libraries in NATURE BIOTECHNOLOGY
  • 2020-08-12. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling in NATURE BIOTECHNOLOGY
  • 2019-12-23. Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins in NATURE BIOTECHNOLOGY
  • 2019-06-17. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices in NATURE METHODS
  • 2018-04-02. Integrating single-cell transcriptomic data across different conditions, technologies, and species in NATURE BIOTECHNOLOGY
  • 2019-04-22. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells in NATURE METHODS
  • 2019-08-02. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion in NATURE BIOTECHNOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41587-021-01065-5

    DOI

    http://dx.doi.org/10.1038/s41587-021-01065-5

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1142019539

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/34675424


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Bacteriophages", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "COVID-19", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chromatin", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "SARS-CoV-2", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Single-Cell Analysis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Spike Glycoprotein, Coronavirus", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Fiskin", 
            "givenName": "Evgenij", 
            "id": "sg:person.01166024661.88", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01166024661.88"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Departments of Pathology, Stanford University, Stanford, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.168010.e", 
              "name": [
                "Departments of Pathology, Stanford University, Stanford, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lareau", 
            "givenName": "Caleb A.", 
            "id": "sg:person.0700325643.61", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700325643.61"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany", 
              "id": "http://www.grid.ac/institutes/grid.419491.0", 
              "name": [
                "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA", 
                "Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ludwig", 
            "givenName": "Leif S.", 
            "id": "sg:person.01240077561.87", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01240077561.87"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Eraslan", 
            "givenName": "G\u00f6kcen", 
            "id": "sg:person.07560514047.23", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07560514047.23"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA", 
              "id": "http://www.grid.ac/institutes/grid.47100.32", 
              "name": [
                "Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Liu", 
            "givenName": "Feimei", 
            "id": "sg:person.011701666441.19", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011701666441.19"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA", 
              "id": "http://www.grid.ac/institutes/grid.47100.32", 
              "name": [
                "Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA", 
                "Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ring", 
            "givenName": "Aaron M.", 
            "id": "sg:person.0577252063.56", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0577252063.56"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.38142.3c", 
              "name": [
                "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA", 
                "Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA", 
                "Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Xavier", 
            "givenName": "Ramnik J.", 
            "id": "sg:person.0717130066.82", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717130066.82"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Genentech, South San Francisco, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.418158.1", 
              "name": [
                "Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA", 
                "Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA", 
                "Genentech, South San Francisco, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Regev", 
            "givenName": "Aviv", 
            "id": "sg:person.01311753732.26", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01311753732.26"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/nmeth.4380", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1090931185", 
              "https://doi.org/10.1038/nmeth.4380"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-019-0372-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123601397", 
              "https://doi.org/10.1038/s41587-019-0372-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41577-020-00480-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1133594378", 
              "https://doi.org/10.1038/s41577-020-00480-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-021-00927-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1138570323", 
              "https://doi.org/10.1038/s41587-021-00927-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-020-0820-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1127346179", 
              "https://doi.org/10.1038/s41592-020-0820-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt1126", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021065956", 
              "https://doi.org/10.1038/nbt1126"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3973", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091383017", 
              "https://doi.org/10.1038/nbt.3973"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41594-018-0028-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1100951741", 
              "https://doi.org/10.1038/s41594-018-0028-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-019-0392-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1113618138", 
              "https://doi.org/10.1038/s41592-019-0392-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-018-1603-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1110764498", 
              "https://doi.org/10.1186/s13059-018-1603-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.1791", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047787000", 
              "https://doi.org/10.1038/nbt.1791"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-019-0206-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1120025484", 
              "https://doi.org/10.1038/s41587-019-0206-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth953", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012346597", 
              "https://doi.org/10.1038/nmeth953"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-020-0645-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1130045868", 
              "https://doi.org/10.1038/s41587-020-0645-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-019-0147-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1117483242", 
              "https://doi.org/10.1038/s41587-019-0147-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-019-0433-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1117288825", 
              "https://doi.org/10.1038/s41592-019-0433-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.4096", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101885942", 
              "https://doi.org/10.1038/nbt.4096"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2021-10-21", 
        "datePublishedReg": "2021-10-21", 
        "description": "Multimodal measurements of single-cell profiles are proving increasingly useful for characterizing cell states and regulatory mechanisms. In the present study, we developed PHAGE-ATAC (Assay for Transposase-Accessible Chromatin), a massively parallel droplet-based method that uses phage displaying, engineered, camelid single-domain antibodies (\u2018nanobodies\u2019) for simultaneous single-cell measurements of protein levels and chromatin accessibility profiles, and mitochondrial DNA-based clonal tracing. We use PHAGE-ATAC for multimodal analysis in primary human immune cells, sample multiplexing, intracellular protein analysis and the detection of SARS-CoV-2 spike protein in human cell populations. Finally, we construct a synthetic high-complexity phage library for selection of antigen-specific nanobodies that bind cells of particular molecular profiles, opening an avenue for protein detection, cell characterization and screening with single-cell genomics.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/s41587-021-01065-5", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.5244369", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1115214", 
            "issn": [
              "1087-0156", 
              "1546-1696"
            ], 
            "name": "Nature Biotechnology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "3", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "40"
          }
        ], 
        "keywords": [
          "simultaneous single-cell measurements", 
          "chromatin accessibility profiles", 
          "single-cell genomics", 
          "intracellular protein analysis", 
          "single-cell profiling", 
          "single-cell profiles", 
          "single-cell measurements", 
          "antigen-specific nanobodies", 
          "chromatin accessibility", 
          "human cell populations", 
          "mitochondrial DNA", 
          "accessibility profiles", 
          "cell states", 
          "regulatory mechanisms", 
          "particular molecular profiles", 
          "clonal tracing", 
          "primary human immune cells", 
          "droplet-based method", 
          "sample multiplexing", 
          "camelid single-domain antibodies", 
          "bind cells", 
          "protein analysis", 
          "protein levels", 
          "cell populations", 
          "phage library", 
          "SARS-CoV-2 spike protein", 
          "molecular profile", 
          "protein", 
          "single-domain antibodies", 
          "protein detection", 
          "spike protein", 
          "human immune cells", 
          "cells", 
          "genomics", 
          "cell characterization", 
          "immune cells", 
          "DNA", 
          "profiling", 
          "nanobodies", 
          "present study", 
          "library", 
          "profile", 
          "mechanism", 
          "selection", 
          "population", 
          "characterization", 
          "avenues", 
          "analysis", 
          "antibodies", 
          "multimodal measurements", 
          "accessibility", 
          "levels", 
          "study", 
          "detection", 
          "tracing", 
          "multiplexing", 
          "multimodal analysis", 
          "state", 
          "displaying", 
          "method", 
          "measurements"
        ], 
        "name": "Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC", 
        "pagination": "374-381", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1142019539"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/s41587-021-01065-5"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "34675424"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/s41587-021-01065-5", 
          "https://app.dimensions.ai/details/publication/pub.1142019539"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-09-02T16:07", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220902/entities/gbq_results/article/article_921.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/s41587-021-01065-5"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41587-021-01065-5'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41587-021-01065-5'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41587-021-01065-5'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41587-021-01065-5'


     

    This table displays all metadata directly associated to this object as RDF triples.

    291 TRIPLES      21 PREDICATES      110 URIs      85 LITERALS      14 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/s41587-021-01065-5 schema:about N395525fc539f4fd984a40c7ba4ebfa48
    2 N3a925f60e9a94ae09313332ff2e5cf79
    3 N924242bb1971475e96bb747b07d136e6
    4 Na24c59ac5f5b4afaa50f3c6144715884
    5 Na6ee098e5a58409b9382f1e477c6bbbe
    6 Nd12c973192914d40b08a4d6bb2be5a8d
    7 Nf00f261ad41244fdacb5a8d78efb24f8
    8 anzsrc-for:06
    9 anzsrc-for:0604
    10 schema:author N901e0e9b98ca4b58ad4309c50dc9894d
    11 schema:citation sg:pub.10.1038/nbt.1791
    12 sg:pub.10.1038/nbt.3973
    13 sg:pub.10.1038/nbt.4096
    14 sg:pub.10.1038/nbt1126
    15 sg:pub.10.1038/nmeth.4380
    16 sg:pub.10.1038/nmeth953
    17 sg:pub.10.1038/s41577-020-00480-0
    18 sg:pub.10.1038/s41587-019-0147-6
    19 sg:pub.10.1038/s41587-019-0206-z
    20 sg:pub.10.1038/s41587-019-0372-z
    21 sg:pub.10.1038/s41587-020-0645-6
    22 sg:pub.10.1038/s41587-021-00927-2
    23 sg:pub.10.1038/s41592-019-0392-0
    24 sg:pub.10.1038/s41592-019-0433-8
    25 sg:pub.10.1038/s41592-020-0820-1
    26 sg:pub.10.1038/s41594-018-0028-6
    27 sg:pub.10.1186/s13059-018-1603-1
    28 schema:datePublished 2021-10-21
    29 schema:datePublishedReg 2021-10-21
    30 schema:description Multimodal measurements of single-cell profiles are proving increasingly useful for characterizing cell states and regulatory mechanisms. In the present study, we developed PHAGE-ATAC (Assay for Transposase-Accessible Chromatin), a massively parallel droplet-based method that uses phage displaying, engineered, camelid single-domain antibodies (‘nanobodies’) for simultaneous single-cell measurements of protein levels and chromatin accessibility profiles, and mitochondrial DNA-based clonal tracing. We use PHAGE-ATAC for multimodal analysis in primary human immune cells, sample multiplexing, intracellular protein analysis and the detection of SARS-CoV-2 spike protein in human cell populations. Finally, we construct a synthetic high-complexity phage library for selection of antigen-specific nanobodies that bind cells of particular molecular profiles, opening an avenue for protein detection, cell characterization and screening with single-cell genomics.
    31 schema:genre article
    32 schema:isAccessibleForFree true
    33 schema:isPartOf N9cb9dd335695440db326fdedf8f87ca7
    34 Nc7862c54f1784709b9b484b8bac160c8
    35 sg:journal.1115214
    36 schema:keywords DNA
    37 SARS-CoV-2 spike protein
    38 accessibility
    39 accessibility profiles
    40 analysis
    41 antibodies
    42 antigen-specific nanobodies
    43 avenues
    44 bind cells
    45 camelid single-domain antibodies
    46 cell characterization
    47 cell populations
    48 cell states
    49 cells
    50 characterization
    51 chromatin accessibility
    52 chromatin accessibility profiles
    53 clonal tracing
    54 detection
    55 displaying
    56 droplet-based method
    57 genomics
    58 human cell populations
    59 human immune cells
    60 immune cells
    61 intracellular protein analysis
    62 levels
    63 library
    64 measurements
    65 mechanism
    66 method
    67 mitochondrial DNA
    68 molecular profile
    69 multimodal analysis
    70 multimodal measurements
    71 multiplexing
    72 nanobodies
    73 particular molecular profiles
    74 phage library
    75 population
    76 present study
    77 primary human immune cells
    78 profile
    79 profiling
    80 protein
    81 protein analysis
    82 protein detection
    83 protein levels
    84 regulatory mechanisms
    85 sample multiplexing
    86 selection
    87 simultaneous single-cell measurements
    88 single-cell genomics
    89 single-cell measurements
    90 single-cell profiles
    91 single-cell profiling
    92 single-domain antibodies
    93 spike protein
    94 state
    95 study
    96 tracing
    97 schema:name Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC
    98 schema:pagination 374-381
    99 schema:productId N603a398677fb4db29622a8747e5b4635
    100 Ncda9ae59ff174a39ac1a28928a0a64b9
    101 Ndb9767e5b8a445b993eca0faab8a3c9a
    102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1142019539
    103 https://doi.org/10.1038/s41587-021-01065-5
    104 schema:sdDatePublished 2022-09-02T16:07
    105 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    106 schema:sdPublisher Nd50a4a2d95864c7cba2e9b39d3732419
    107 schema:url https://doi.org/10.1038/s41587-021-01065-5
    108 sgo:license sg:explorer/license/
    109 sgo:sdDataset articles
    110 rdf:type schema:ScholarlyArticle
    111 N08f0d082895242b4a16c23eeea035fcc rdf:first sg:person.0577252063.56
    112 rdf:rest N1c98f3a4fa504b5f81dad472e25e509b
    113 N1c98f3a4fa504b5f81dad472e25e509b rdf:first sg:person.0717130066.82
    114 rdf:rest N1ebd33daa972482a881f5635ad56372b
    115 N1ebd33daa972482a881f5635ad56372b rdf:first sg:person.01311753732.26
    116 rdf:rest rdf:nil
    117 N395525fc539f4fd984a40c7ba4ebfa48 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    118 schema:name Spike Glycoprotein, Coronavirus
    119 rdf:type schema:DefinedTerm
    120 N3a925f60e9a94ae09313332ff2e5cf79 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    121 schema:name SARS-CoV-2
    122 rdf:type schema:DefinedTerm
    123 N3d558bcd01024581a250c38fdf4ca001 rdf:first sg:person.07560514047.23
    124 rdf:rest Na3ed674044bc44a2be0a5bdfc3c78eef
    125 N5f6bef8fbfc341ad858ded12d53f68aa rdf:first sg:person.01240077561.87
    126 rdf:rest N3d558bcd01024581a250c38fdf4ca001
    127 N603a398677fb4db29622a8747e5b4635 schema:name doi
    128 schema:value 10.1038/s41587-021-01065-5
    129 rdf:type schema:PropertyValue
    130 N901e0e9b98ca4b58ad4309c50dc9894d rdf:first sg:person.01166024661.88
    131 rdf:rest Ne7aee59a04f546eca23988f917f8dd94
    132 N924242bb1971475e96bb747b07d136e6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    133 schema:name Bacteriophages
    134 rdf:type schema:DefinedTerm
    135 N9cb9dd335695440db326fdedf8f87ca7 schema:volumeNumber 40
    136 rdf:type schema:PublicationVolume
    137 Na24c59ac5f5b4afaa50f3c6144715884 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    138 schema:name Humans
    139 rdf:type schema:DefinedTerm
    140 Na3ed674044bc44a2be0a5bdfc3c78eef rdf:first sg:person.011701666441.19
    141 rdf:rest N08f0d082895242b4a16c23eeea035fcc
    142 Na6ee098e5a58409b9382f1e477c6bbbe schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    143 schema:name COVID-19
    144 rdf:type schema:DefinedTerm
    145 Nc7862c54f1784709b9b484b8bac160c8 schema:issueNumber 3
    146 rdf:type schema:PublicationIssue
    147 Ncda9ae59ff174a39ac1a28928a0a64b9 schema:name pubmed_id
    148 schema:value 34675424
    149 rdf:type schema:PropertyValue
    150 Nd12c973192914d40b08a4d6bb2be5a8d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    151 schema:name Single-Cell Analysis
    152 rdf:type schema:DefinedTerm
    153 Nd50a4a2d95864c7cba2e9b39d3732419 schema:name Springer Nature - SN SciGraph project
    154 rdf:type schema:Organization
    155 Ndb9767e5b8a445b993eca0faab8a3c9a schema:name dimensions_id
    156 schema:value pub.1142019539
    157 rdf:type schema:PropertyValue
    158 Ne7aee59a04f546eca23988f917f8dd94 rdf:first sg:person.0700325643.61
    159 rdf:rest N5f6bef8fbfc341ad858ded12d53f68aa
    160 Nf00f261ad41244fdacb5a8d78efb24f8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    161 schema:name Chromatin
    162 rdf:type schema:DefinedTerm
    163 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    164 schema:name Biological Sciences
    165 rdf:type schema:DefinedTerm
    166 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    167 schema:name Genetics
    168 rdf:type schema:DefinedTerm
    169 sg:grant.5244369 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-021-01065-5
    170 rdf:type schema:MonetaryGrant
    171 sg:journal.1115214 schema:issn 1087-0156
    172 1546-1696
    173 schema:name Nature Biotechnology
    174 schema:publisher Springer Nature
    175 rdf:type schema:Periodical
    176 sg:person.01166024661.88 schema:affiliation grid-institutes:grid.66859.34
    177 schema:familyName Fiskin
    178 schema:givenName Evgenij
    179 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01166024661.88
    180 rdf:type schema:Person
    181 sg:person.011701666441.19 schema:affiliation grid-institutes:grid.47100.32
    182 schema:familyName Liu
    183 schema:givenName Feimei
    184 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011701666441.19
    185 rdf:type schema:Person
    186 sg:person.01240077561.87 schema:affiliation grid-institutes:grid.419491.0
    187 schema:familyName Ludwig
    188 schema:givenName Leif S.
    189 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01240077561.87
    190 rdf:type schema:Person
    191 sg:person.01311753732.26 schema:affiliation grid-institutes:grid.418158.1
    192 schema:familyName Regev
    193 schema:givenName Aviv
    194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01311753732.26
    195 rdf:type schema:Person
    196 sg:person.0577252063.56 schema:affiliation grid-institutes:grid.47100.32
    197 schema:familyName Ring
    198 schema:givenName Aaron M.
    199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0577252063.56
    200 rdf:type schema:Person
    201 sg:person.0700325643.61 schema:affiliation grid-institutes:grid.168010.e
    202 schema:familyName Lareau
    203 schema:givenName Caleb A.
    204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700325643.61
    205 rdf:type schema:Person
    206 sg:person.0717130066.82 schema:affiliation grid-institutes:grid.38142.3c
    207 schema:familyName Xavier
    208 schema:givenName Ramnik J.
    209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717130066.82
    210 rdf:type schema:Person
    211 sg:person.07560514047.23 schema:affiliation grid-institutes:grid.66859.34
    212 schema:familyName Eraslan
    213 schema:givenName Gökcen
    214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07560514047.23
    215 rdf:type schema:Person
    216 sg:pub.10.1038/nbt.1791 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047787000
    217 https://doi.org/10.1038/nbt.1791
    218 rdf:type schema:CreativeWork
    219 sg:pub.10.1038/nbt.3973 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091383017
    220 https://doi.org/10.1038/nbt.3973
    221 rdf:type schema:CreativeWork
    222 sg:pub.10.1038/nbt.4096 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101885942
    223 https://doi.org/10.1038/nbt.4096
    224 rdf:type schema:CreativeWork
    225 sg:pub.10.1038/nbt1126 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021065956
    226 https://doi.org/10.1038/nbt1126
    227 rdf:type schema:CreativeWork
    228 sg:pub.10.1038/nmeth.4380 schema:sameAs https://app.dimensions.ai/details/publication/pub.1090931185
    229 https://doi.org/10.1038/nmeth.4380
    230 rdf:type schema:CreativeWork
    231 sg:pub.10.1038/nmeth953 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012346597
    232 https://doi.org/10.1038/nmeth953
    233 rdf:type schema:CreativeWork
    234 sg:pub.10.1038/s41577-020-00480-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1133594378
    235 https://doi.org/10.1038/s41577-020-00480-0
    236 rdf:type schema:CreativeWork
    237 sg:pub.10.1038/s41587-019-0147-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1117483242
    238 https://doi.org/10.1038/s41587-019-0147-6
    239 rdf:type schema:CreativeWork
    240 sg:pub.10.1038/s41587-019-0206-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1120025484
    241 https://doi.org/10.1038/s41587-019-0206-z
    242 rdf:type schema:CreativeWork
    243 sg:pub.10.1038/s41587-019-0372-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1123601397
    244 https://doi.org/10.1038/s41587-019-0372-z
    245 rdf:type schema:CreativeWork
    246 sg:pub.10.1038/s41587-020-0645-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1130045868
    247 https://doi.org/10.1038/s41587-020-0645-6
    248 rdf:type schema:CreativeWork
    249 sg:pub.10.1038/s41587-021-00927-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1138570323
    250 https://doi.org/10.1038/s41587-021-00927-2
    251 rdf:type schema:CreativeWork
    252 sg:pub.10.1038/s41592-019-0392-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1113618138
    253 https://doi.org/10.1038/s41592-019-0392-0
    254 rdf:type schema:CreativeWork
    255 sg:pub.10.1038/s41592-019-0433-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1117288825
    256 https://doi.org/10.1038/s41592-019-0433-8
    257 rdf:type schema:CreativeWork
    258 sg:pub.10.1038/s41592-020-0820-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1127346179
    259 https://doi.org/10.1038/s41592-020-0820-1
    260 rdf:type schema:CreativeWork
    261 sg:pub.10.1038/s41594-018-0028-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1100951741
    262 https://doi.org/10.1038/s41594-018-0028-6
    263 rdf:type schema:CreativeWork
    264 sg:pub.10.1186/s13059-018-1603-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110764498
    265 https://doi.org/10.1186/s13059-018-1603-1
    266 rdf:type schema:CreativeWork
    267 grid-institutes:grid.168010.e schema:alternateName Departments of Pathology, Stanford University, Stanford, CA, USA
    268 schema:name Departments of Pathology, Stanford University, Stanford, CA, USA
    269 rdf:type schema:Organization
    270 grid-institutes:grid.38142.3c schema:alternateName Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
    271 schema:name Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
    272 Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
    273 Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
    274 rdf:type schema:Organization
    275 grid-institutes:grid.418158.1 schema:alternateName Genentech, South San Francisco, CA, USA
    276 schema:name Genentech, South San Francisco, CA, USA
    277 Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
    278 Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
    279 rdf:type schema:Organization
    280 grid-institutes:grid.419491.0 schema:alternateName Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
    281 schema:name Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
    282 Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
    283 rdf:type schema:Organization
    284 grid-institutes:grid.47100.32 schema:alternateName Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
    285 Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
    286 schema:name Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
    287 Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
    288 rdf:type schema:Organization
    289 grid-institutes:grid.66859.34 schema:alternateName Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
    290 schema:name Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
    291 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...