Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step. View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2019

AUTHORS

Hannes Schroeder , Peter de Barros Damgaard , Morten E Allentoft

ABSTRACT

Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction. More... »

PAGES

21-24

References to SciGraph publications

Book

TITLE

Ancient DNA

ISBN

978-1-4939-9175-4
978-1-4939-9176-1

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-4939-9176-1_3

DOI

http://dx.doi.org/10.1007/978-1-4939-9176-1_3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112770933

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30875040


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"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. hschroeder@snm.ku.dk."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schroeder", 
        "givenName": "Hannes", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark."
          ], 
          "type": "Organization"
        }, 
        "familyName": "de Barros Damgaard", 
        "givenName": "Peter", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Allentoft", 
        "givenName": "Morten E", 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1093/molbev/msi195", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011247579"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msi195", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011247579"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/srep11184", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015447928", 
          "https://doi.org/10.1038/srep11184"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/1755-0998.12623", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036288145"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.aanat.2011.07.003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037337752"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ncomms6257", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037347132", 
          "https://doi.org/10.1038/ncomms6257"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.forsciint.2004.11.017", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039359779"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2144/000114320", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1069096806"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019", 
    "datePublishedReg": "2019-01-01", 
    "description": "Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.", 
    "editor": [
      {
        "familyName": "Shapiro", 
        "givenName": "Beth", 
        "type": "Person"
      }, 
      {
        "familyName": "Barlow", 
        "givenName": "Axel", 
        "type": "Person"
      }, 
      {
        "familyName": "Heintzman", 
        "givenName": "Peter D.", 
        "type": "Person"
      }, 
      {
        "familyName": "Hofreiter", 
        "givenName": "Michael", 
        "type": "Person"
      }, 
      {
        "familyName": "Paijmans", 
        "givenName": "Johanna L. A.", 
        "type": "Person"
      }, 
      {
        "familyName": "Soares", 
        "givenName": "Andr\u00e9 E. R.", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-4939-9176-1_3", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-1-4939-9175-4", 
        "978-1-4939-9176-1"
      ], 
      "name": "Ancient DNA", 
      "type": "Book"
    }, 
    "name": "Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step.", 
    "pagination": "21-24", 
    "productId": [
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30875040"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1112770933"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-4939-9176-1_3"
        ]
      }
    ], 
    "publisher": {
      "location": "New York, NY", 
      "name": "Springer New York", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-4939-9176-1_3", 
      "https://app.dimensions.ai/details/publication/pub.1112770933"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-16T10:08", 
    "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/v90/0000000377_0000000377/records_106813_00000002.jsonl", 
    "type": "Chapter", 
    "url": "http://link.springer.com/10.1007/978-1-4939-9176-1_3"
  }
]
 

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.10.1007/978-1-4939-9176-1_3'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-9176-1_3'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-9176-1_3'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-9176-1_3'


 

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

125 TRIPLES      23 PREDICATES      34 URIs      20 LITERALS      8 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-4939-9176-1_3 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N605226ee433249e49836e04503fe4567
4 schema:citation sg:pub.10.1038/ncomms6257
5 sg:pub.10.1038/srep11184
6 https://doi.org/10.1016/j.aanat.2011.07.003
7 https://doi.org/10.1016/j.forsciint.2004.11.017
8 https://doi.org/10.1093/molbev/msi195
9 https://doi.org/10.1111/1755-0998.12623
10 https://doi.org/10.2144/000114320
11 schema:datePublished 2019
12 schema:datePublishedReg 2019-01-01
13 schema:description Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.
14 schema:editor Nfe8cb595611e4e38b91c237ae363ca23
15 schema:genre chapter
16 schema:inLanguage en
17 schema:isAccessibleForFree false
18 schema:isPartOf N387e88bc5f174ee99920075e7490021e
19 schema:name Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step.
20 schema:pagination 21-24
21 schema:productId N6e3b160680e7460a8624969d556a63f1
22 Nd22fecaa53c244ce99e2f9f99e8a3df9
23 Nf500070561ca46b292798f8ead896028
24 schema:publisher N2dc0ed2b2fa04e7ca3c9fe2e7240a11e
25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112770933
26 https://doi.org/10.1007/978-1-4939-9176-1_3
27 schema:sdDatePublished 2019-04-16T10:08
28 schema:sdLicense https://scigraph.springernature.com/explorer/license/
29 schema:sdPublisher N345c6cc3e12c492789257f4ff17bd546
30 schema:url http://link.springer.com/10.1007/978-1-4939-9176-1_3
31 sgo:license sg:explorer/license/
32 sgo:sdDataset chapters
33 rdf:type schema:Chapter
34 N07ef70400e224e7ab491483878b6b002 rdf:first N8eb9a847ef864007a89c52543aa8a05c
35 rdf:rest Nd0b5b1f5e38e479598471aec426595f9
36 N0e124c504923494a8e74a43ecbf905ff rdf:first N4791d56b377146b9ab0f4f55b5ac7c2c
37 rdf:rest Nb31cb6a87fda42a49952d4b0a666d5e9
38 N22aca98578fc4ec7af749ff0aa416f40 rdf:first N5a35449792f444929893aaf590693611
39 rdf:rest Ne1e4be3f38494249a35eab1b3512c8e4
40 N2781a399837f42588dab3a1f042b522f schema:affiliation https://www.grid.ac/institutes/grid.5254.6
41 schema:familyName Allentoft
42 schema:givenName Morten E
43 rdf:type schema:Person
44 N2dc0ed2b2fa04e7ca3c9fe2e7240a11e schema:location New York, NY
45 schema:name Springer New York
46 rdf:type schema:Organisation
47 N345c6cc3e12c492789257f4ff17bd546 schema:name Springer Nature - SN SciGraph project
48 rdf:type schema:Organization
49 N387e88bc5f174ee99920075e7490021e schema:isbn 978-1-4939-9175-4
50 978-1-4939-9176-1
51 schema:name Ancient DNA
52 rdf:type schema:Book
53 N441e71d2eb4b4b2caa70a7e459fe5ceb rdf:first Nda70030c913040ac94ddd752e75fde5e
54 rdf:rest N07ef70400e224e7ab491483878b6b002
55 N4791d56b377146b9ab0f4f55b5ac7c2c schema:affiliation https://www.grid.ac/institutes/grid.5254.6
56 schema:familyName de Barros Damgaard
57 schema:givenName Peter
58 rdf:type schema:Person
59 N56fa81553d2245429fdaf5ec42d613a6 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
60 schema:familyName Schroeder
61 schema:givenName Hannes
62 rdf:type schema:Person
63 N5a35449792f444929893aaf590693611 schema:familyName Paijmans
64 schema:givenName Johanna L. A.
65 rdf:type schema:Person
66 N605226ee433249e49836e04503fe4567 rdf:first N56fa81553d2245429fdaf5ec42d613a6
67 rdf:rest N0e124c504923494a8e74a43ecbf905ff
68 N6e3b160680e7460a8624969d556a63f1 schema:name pubmed_id
69 schema:value 30875040
70 rdf:type schema:PropertyValue
71 N8eb9a847ef864007a89c52543aa8a05c schema:familyName Heintzman
72 schema:givenName Peter D.
73 rdf:type schema:Person
74 N8fe412e496e3441bafe6637f7b1778f3 schema:familyName Hofreiter
75 schema:givenName Michael
76 rdf:type schema:Person
77 N926c271c81eb4def9cafaed5e3c8ac62 schema:familyName Shapiro
78 schema:givenName Beth
79 rdf:type schema:Person
80 N935e589bb262473f8152b3309348d198 schema:familyName Soares
81 schema:givenName André E. R.
82 rdf:type schema:Person
83 Nb31cb6a87fda42a49952d4b0a666d5e9 rdf:first N2781a399837f42588dab3a1f042b522f
84 rdf:rest rdf:nil
85 Nd0b5b1f5e38e479598471aec426595f9 rdf:first N8fe412e496e3441bafe6637f7b1778f3
86 rdf:rest N22aca98578fc4ec7af749ff0aa416f40
87 Nd22fecaa53c244ce99e2f9f99e8a3df9 schema:name dimensions_id
88 schema:value pub.1112770933
89 rdf:type schema:PropertyValue
90 Nda70030c913040ac94ddd752e75fde5e schema:familyName Barlow
91 schema:givenName Axel
92 rdf:type schema:Person
93 Ne1e4be3f38494249a35eab1b3512c8e4 rdf:first N935e589bb262473f8152b3309348d198
94 rdf:rest rdf:nil
95 Nf500070561ca46b292798f8ead896028 schema:name doi
96 schema:value 10.1007/978-1-4939-9176-1_3
97 rdf:type schema:PropertyValue
98 Nfe8cb595611e4e38b91c237ae363ca23 rdf:first N926c271c81eb4def9cafaed5e3c8ac62
99 rdf:rest N441e71d2eb4b4b2caa70a7e459fe5ceb
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:pub.10.1038/ncomms6257 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037347132
107 https://doi.org/10.1038/ncomms6257
108 rdf:type schema:CreativeWork
109 sg:pub.10.1038/srep11184 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015447928
110 https://doi.org/10.1038/srep11184
111 rdf:type schema:CreativeWork
112 https://doi.org/10.1016/j.aanat.2011.07.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037337752
113 rdf:type schema:CreativeWork
114 https://doi.org/10.1016/j.forsciint.2004.11.017 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039359779
115 rdf:type schema:CreativeWork
116 https://doi.org/10.1093/molbev/msi195 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011247579
117 rdf:type schema:CreativeWork
118 https://doi.org/10.1111/1755-0998.12623 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036288145
119 rdf:type schema:CreativeWork
120 https://doi.org/10.2144/000114320 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069096806
121 rdf:type schema:CreativeWork
122 https://www.grid.ac/institutes/grid.5254.6 schema:alternateName University of Copenhagen
123 schema:name Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
124 Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. hschroeder@snm.ku.dk.
125 rdf:type schema:Organization
 




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


...