A Phenol–Chloroform Protocol for Extracting DNA from Ancient Samples View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2012

AUTHORS

Ross Barnett , Greger Larson

ABSTRACT

The myriad downstream applications of ancient DNA (aDNA) analysis all ultimately require that sequence data are generated from extracts of ancient material. DNA extraction from tissues known to contain preserved biomolecules (e.g. teeth, hair, tissue, bone) relies on subtle modifications of a basic technique that has been in use for nearly two decades. Multiple DNA extraction protocols have been introduced, with varying levels of success depending on tissue type and the long-term preservation environment to which the ancient tissue was exposed. Here, we describe the phenol-chloroform method for extracting aDNA from any tissue type. This commonly employed method allows for the recovery of total nucleic acid content with minimal loss of low molecular weight double-stranded DNA. More... »

PAGES

13-19

References to SciGraph publications

  • 2007-07. Ancient DNA extraction from bones and teeth in NATURE PROTOCOLS
  • 1993-04. Instability and decay of the primary structure of DNA in NATURE
  • 1989-11. Ancient bone DNA amplified in NATURE
  • 1994-06. Ancient DNA: Methodological challenges in CELLULAR AND MOLECULAR LIFE SCIENCES
  • 2001-05. Ancient DNA in NATURE REVIEWS GENETICS
  • 1996-07. An agent cleaving glucose-derived protein crosslinks in vitro and in vivo in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_2

    DOI

    http://dx.doi.org/10.1007/978-1-61779-516-9_2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1040904652

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22237516


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "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"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chelating Agents", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Chloroform", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genetic Techniques", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Paleontology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phenol", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Durham University", 
              "id": "https://www.grid.ac/institutes/grid.8250.f", 
              "name": [
                "Department of Archaeology, Durham University, South Road, Durham, DH1 3LE, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Barnett", 
            "givenName": "Ross", 
            "id": "sg:person.01046770114.08", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01046770114.08"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Durham University", 
              "id": "https://www.grid.ac/institutes/grid.8250.f", 
              "name": [
                "Department of Archaeology, Durham University, South Road, Durham, DH1 3LE, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Larson", 
            "givenName": "Greger", 
            "id": "sg:person.01036713610.39", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01036713610.39"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1016/j.jas.2006.10.023", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016800120"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/362709a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019428971", 
              "https://doi.org/10.1038/362709a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/342485a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026831600", 
              "https://doi.org/10.1038/342485a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1098/rspb.1991.0049", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033575358"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jas.2010.11.010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035132881"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35072071", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037967401", 
              "https://doi.org/10.1038/35072071"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35072071", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037967401", 
              "https://doi.org/10.1038/35072071"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/382275a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045140965", 
              "https://doi.org/10.1038/382275a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nprot.2007.247", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047432076", 
              "https://doi.org/10.1038/nprot.2007.247"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cub.2004.06.008", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047857198"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf01921720", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053589205", 
              "https://doi.org/10.1007/bf01921720"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf01921720", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053589205", 
              "https://doi.org/10.1007/bf01921720"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/ar000207x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1055148333"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/ar000207x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1055148333"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.289.5482.1139b", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062570650"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.2144/000112383", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1069095463"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2012", 
        "datePublishedReg": "2012-01-01", 
        "description": "The myriad downstream applications of ancient DNA (aDNA) analysis all ultimately require that sequence data are generated from extracts of ancient material. DNA extraction from tissues known to contain preserved biomolecules (e.g. teeth, hair, tissue, bone) relies on subtle modifications of a basic technique that has been in use for nearly two decades. Multiple DNA extraction protocols have been introduced, with varying levels of success depending on tissue type and the long-term preservation environment to which the ancient tissue was exposed. Here, we describe the phenol-chloroform method for extracting aDNA from any tissue type. This commonly employed method allows for the recovery of total nucleic acid content with minimal loss of low molecular weight double-stranded DNA.", 
        "editor": [
          {
            "familyName": "Shapiro", 
            "givenName": "Beth", 
            "type": "Person"
          }, 
          {
            "familyName": "Hofreiter", 
            "givenName": "Michael", 
            "type": "Person"
          }
        ], 
        "genre": "chapter", 
        "id": "sg:pub.10.1007/978-1-61779-516-9_2", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": false, 
        "isPartOf": {
          "isbn": [
            "978-1-61779-515-2", 
            "978-1-61779-516-9"
          ], 
          "name": "Ancient DNA", 
          "type": "Book"
        }, 
        "name": "A Phenol\u2013Chloroform Protocol for Extracting DNA from Ancient Samples", 
        "pagination": "13-19", 
        "productId": [
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/978-1-61779-516-9_2"
            ]
          }, 
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "c2db002758ed5936dfd11f05b1deaa541e64445c530a799f7ce2a2aad67e993a"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1040904652"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "22237516"
            ]
          }
        ], 
        "publisher": {
          "location": "Totowa, NJ", 
          "name": "Humana Press", 
          "type": "Organisation"
        }, 
        "sameAs": [
          "https://doi.org/10.1007/978-1-61779-516-9_2", 
          "https://app.dimensions.ai/details/publication/pub.1040904652"
        ], 
        "sdDataset": "chapters", 
        "sdDatePublished": "2019-04-16T00:50", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8700_00000268.jsonl", 
        "type": "Chapter", 
        "url": "http://link.springer.com/10.1007/978-1-61779-516-9_2"
      }
    ]
     

    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.10.1007/978-1-61779-516-9_2'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_2'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_2'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_2'


     

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

    150 TRIPLES      23 PREDICATES      47 URIs      27 LITERALS      15 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/978-1-61779-516-9_2 schema:about N25d144a63fb94f42bf969df56acd1769
    2 N6fbaf7b6f92c4051a0363479cc0c74cc
    3 N851cc935cb9f4e0a92ce0b3ada928107
    4 N9c47d03276bc408d805c6b219b684e1e
    5 N9f8457cf3449476596fa908dc34856c5
    6 Nfb6fe6c3259a43929f6b136b5e3d920b
    7 anzsrc-for:06
    8 anzsrc-for:0604
    9 schema:author Ne9aa07e28e0e46078c0aca2f3c6134a0
    10 schema:citation sg:pub.10.1007/bf01921720
    11 sg:pub.10.1038/342485a0
    12 sg:pub.10.1038/35072071
    13 sg:pub.10.1038/362709a0
    14 sg:pub.10.1038/382275a0
    15 sg:pub.10.1038/nprot.2007.247
    16 https://doi.org/10.1016/j.cub.2004.06.008
    17 https://doi.org/10.1016/j.jas.2006.10.023
    18 https://doi.org/10.1016/j.jas.2010.11.010
    19 https://doi.org/10.1021/ar000207x
    20 https://doi.org/10.1098/rspb.1991.0049
    21 https://doi.org/10.1126/science.289.5482.1139b
    22 https://doi.org/10.2144/000112383
    23 schema:datePublished 2012
    24 schema:datePublishedReg 2012-01-01
    25 schema:description The myriad downstream applications of ancient DNA (aDNA) analysis all ultimately require that sequence data are generated from extracts of ancient material. DNA extraction from tissues known to contain preserved biomolecules (e.g. teeth, hair, tissue, bone) relies on subtle modifications of a basic technique that has been in use for nearly two decades. Multiple DNA extraction protocols have been introduced, with varying levels of success depending on tissue type and the long-term preservation environment to which the ancient tissue was exposed. Here, we describe the phenol-chloroform method for extracting aDNA from any tissue type. This commonly employed method allows for the recovery of total nucleic acid content with minimal loss of low molecular weight double-stranded DNA.
    26 schema:editor N66648aaf6dfc4dd8ae197e9cfb0a4cfb
    27 schema:genre chapter
    28 schema:inLanguage en
    29 schema:isAccessibleForFree false
    30 schema:isPartOf Na3ecd6671ded427186a538eb73f48a06
    31 schema:name A Phenol–Chloroform Protocol for Extracting DNA from Ancient Samples
    32 schema:pagination 13-19
    33 schema:productId N55c185c079124cdc89da0aa5687c8dca
    34 N62dfccb7806a42e7b5e9943bd1bb7250
    35 N9997006055454456adf5767522e12128
    36 Ne346844217604fc4aa72cfdcc6c9c377
    37 schema:publisher N2a0297dc65044f798b7b65cd32948570
    38 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040904652
    39 https://doi.org/10.1007/978-1-61779-516-9_2
    40 schema:sdDatePublished 2019-04-16T00:50
    41 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    42 schema:sdPublisher Ne915382ce7b94964adc6510296a3bde9
    43 schema:url http://link.springer.com/10.1007/978-1-61779-516-9_2
    44 sgo:license sg:explorer/license/
    45 sgo:sdDataset chapters
    46 rdf:type schema:Chapter
    47 N25d144a63fb94f42bf969df56acd1769 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    48 schema:name Paleontology
    49 rdf:type schema:DefinedTerm
    50 N2a0297dc65044f798b7b65cd32948570 schema:location Totowa, NJ
    51 schema:name Humana Press
    52 rdf:type schema:Organisation
    53 N55c185c079124cdc89da0aa5687c8dca schema:name readcube_id
    54 schema:value c2db002758ed5936dfd11f05b1deaa541e64445c530a799f7ce2a2aad67e993a
    55 rdf:type schema:PropertyValue
    56 N57b5447444d14b0b8154a496fc190104 rdf:first sg:person.01036713610.39
    57 rdf:rest rdf:nil
    58 N62dfccb7806a42e7b5e9943bd1bb7250 schema:name pubmed_id
    59 schema:value 22237516
    60 rdf:type schema:PropertyValue
    61 N658b5483d6614c5fbe1a4123880abe27 rdf:first Nf96d85c275f548409009025076942ca9
    62 rdf:rest rdf:nil
    63 N66648aaf6dfc4dd8ae197e9cfb0a4cfb rdf:first Nf894a031bf3c46bcbdcd02d4ce7781b4
    64 rdf:rest N658b5483d6614c5fbe1a4123880abe27
    65 N6fbaf7b6f92c4051a0363479cc0c74cc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    66 schema:name Genetic Techniques
    67 rdf:type schema:DefinedTerm
    68 N851cc935cb9f4e0a92ce0b3ada928107 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    69 schema:name DNA
    70 rdf:type schema:DefinedTerm
    71 N9997006055454456adf5767522e12128 schema:name dimensions_id
    72 schema:value pub.1040904652
    73 rdf:type schema:PropertyValue
    74 N9c47d03276bc408d805c6b219b684e1e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    75 schema:name Chelating Agents
    76 rdf:type schema:DefinedTerm
    77 N9f8457cf3449476596fa908dc34856c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    78 schema:name Chloroform
    79 rdf:type schema:DefinedTerm
    80 Na3ecd6671ded427186a538eb73f48a06 schema:isbn 978-1-61779-515-2
    81 978-1-61779-516-9
    82 schema:name Ancient DNA
    83 rdf:type schema:Book
    84 Ne346844217604fc4aa72cfdcc6c9c377 schema:name doi
    85 schema:value 10.1007/978-1-61779-516-9_2
    86 rdf:type schema:PropertyValue
    87 Ne915382ce7b94964adc6510296a3bde9 schema:name Springer Nature - SN SciGraph project
    88 rdf:type schema:Organization
    89 Ne9aa07e28e0e46078c0aca2f3c6134a0 rdf:first sg:person.01046770114.08
    90 rdf:rest N57b5447444d14b0b8154a496fc190104
    91 Nf894a031bf3c46bcbdcd02d4ce7781b4 schema:familyName Shapiro
    92 schema:givenName Beth
    93 rdf:type schema:Person
    94 Nf96d85c275f548409009025076942ca9 schema:familyName Hofreiter
    95 schema:givenName Michael
    96 rdf:type schema:Person
    97 Nfb6fe6c3259a43929f6b136b5e3d920b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    98 schema:name Phenol
    99 rdf:type schema:DefinedTerm
    100 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    101 schema:name Biological Sciences
    102 rdf:type schema:DefinedTerm
    103 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    104 schema:name Genetics
    105 rdf:type schema:DefinedTerm
    106 sg:person.01036713610.39 schema:affiliation https://www.grid.ac/institutes/grid.8250.f
    107 schema:familyName Larson
    108 schema:givenName Greger
    109 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01036713610.39
    110 rdf:type schema:Person
    111 sg:person.01046770114.08 schema:affiliation https://www.grid.ac/institutes/grid.8250.f
    112 schema:familyName Barnett
    113 schema:givenName Ross
    114 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01046770114.08
    115 rdf:type schema:Person
    116 sg:pub.10.1007/bf01921720 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053589205
    117 https://doi.org/10.1007/bf01921720
    118 rdf:type schema:CreativeWork
    119 sg:pub.10.1038/342485a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026831600
    120 https://doi.org/10.1038/342485a0
    121 rdf:type schema:CreativeWork
    122 sg:pub.10.1038/35072071 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037967401
    123 https://doi.org/10.1038/35072071
    124 rdf:type schema:CreativeWork
    125 sg:pub.10.1038/362709a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019428971
    126 https://doi.org/10.1038/362709a0
    127 rdf:type schema:CreativeWork
    128 sg:pub.10.1038/382275a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045140965
    129 https://doi.org/10.1038/382275a0
    130 rdf:type schema:CreativeWork
    131 sg:pub.10.1038/nprot.2007.247 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047432076
    132 https://doi.org/10.1038/nprot.2007.247
    133 rdf:type schema:CreativeWork
    134 https://doi.org/10.1016/j.cub.2004.06.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047857198
    135 rdf:type schema:CreativeWork
    136 https://doi.org/10.1016/j.jas.2006.10.023 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016800120
    137 rdf:type schema:CreativeWork
    138 https://doi.org/10.1016/j.jas.2010.11.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035132881
    139 rdf:type schema:CreativeWork
    140 https://doi.org/10.1021/ar000207x schema:sameAs https://app.dimensions.ai/details/publication/pub.1055148333
    141 rdf:type schema:CreativeWork
    142 https://doi.org/10.1098/rspb.1991.0049 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033575358
    143 rdf:type schema:CreativeWork
    144 https://doi.org/10.1126/science.289.5482.1139b schema:sameAs https://app.dimensions.ai/details/publication/pub.1062570650
    145 rdf:type schema:CreativeWork
    146 https://doi.org/10.2144/000112383 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069095463
    147 rdf:type schema:CreativeWork
    148 https://www.grid.ac/institutes/grid.8250.f schema:alternateName Durham University
    149 schema:name Department of Archaeology, Durham University, South Road, Durham, DH1 3LE, UK
    150 rdf:type schema:Organization
     




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


    ...