Other Open Access

DNase-seq and histone mark ChIP-seq convolutional autoencoders

Lekschas, Fritz; Peterson, Brant; Haehn, Daniel; Ma, Eric; Gehlenborg, Nils; Pfister, Hanspeter


DCAT Export

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://doi.org/10.5281/zenodo.2609763">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://doi.org/10.5281/zenodo.2609763</dct:identifier>
    <foaf:page rdf:resource="https://doi.org/10.5281/zenodo.2609763"/>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-8432-4835">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0001-8432-4835</dct:identifier>
        <foaf:name>Lekschas, Fritz</foaf:name>
        <foaf:givenName>Fritz</foaf:givenName>
        <foaf:familyName>Lekschas</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Harvard University</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Peterson, Brant</foaf:name>
        <foaf:givenName>Brant</foaf:givenName>
        <foaf:familyName>Peterson</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Novartis Institutes for BioMedical Research</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-9144-3461">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0001-9144-3461</dct:identifier>
        <foaf:name>Haehn, Daniel</foaf:name>
        <foaf:givenName>Daniel</foaf:givenName>
        <foaf:familyName>Haehn</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Harvard University</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-0041-5989">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0003-0041-5989</dct:identifier>
        <foaf:name>Ma, Eric</foaf:name>
        <foaf:givenName>Eric</foaf:givenName>
        <foaf:familyName>Ma</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Novartis Institutes for BioMedical Research</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-0327-8297">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0003-0327-8297</dct:identifier>
        <foaf:name>Gehlenborg, Nils</foaf:name>
        <foaf:givenName>Nils</foaf:givenName>
        <foaf:familyName>Gehlenborg</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Harvard Medical School</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-3620-2582">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">0000-0002-3620-2582</dct:identifier>
        <foaf:name>Pfister, Hanspeter</foaf:name>
        <foaf:givenName>Hanspeter</foaf:givenName>
        <foaf:familyName>Pfister</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Harvard University</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:title>DNase-seq and histone mark ChIP-seq convolutional autoencoders</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Zenodo</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2019</dct:issued>
    <dcat:keyword>Autoencoder</dcat:keyword>
    <dcat:keyword>CNN</dcat:keyword>
    <dcat:keyword>DNase-seq</dcat:keyword>
    <dcat:keyword>ChIP-seq</dcat:keyword>
    <dcat:keyword>histone mark ChIP-seq</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2019-03-26</dct:issued>
    <owl:sameAs rdf:resource="https://zenodo.org/record/2609763"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/2609763</skos:notation>
        <adms:schemeAgency>url</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <dct:relation rdf:resource="https://doi.org/10.1101/597518"/>
    <dct:isVersionOf rdf:resource="https://doi.org/10.5281/zenodo.2609762"/>
    <owl:versionInfo>1.0.0</owl:versionInfo>
    <dct:description>&lt;p&gt;We provide 6 convolutional autoencoders for encoding DNase-seq and histone mark ChIP-seq regions of 3 kilobase pairs, 12 kilobase pairs, and 120 kilobase pairs at 25 base pair, 100 base pair, and 1000 base pair resolution respectively. The histone mark ChIP-seq autoencoders were trained on 49 experiments from the &lt;a href="http://www.roadmapepigenomics.org"&gt;Roadmap Epigenetics&lt;/a&gt; projects targeting&amp;nbsp;H3K4me1, H3K4me3, H3K27ac, H3K9ac, H3K27me3, H3K9me3, and H3K36me (see experiment IDs below). The DNase-seq autoencoders were trained on 120 experiments from the &lt;a href="https://www.encodeproject.org"&gt;ENCODE projects&lt;/a&gt;&amp;nbsp;(see accession numbers below).&lt;/p&gt; &lt;p&gt;These autoencoders were produced as part of the &lt;a href="http://peax.lekschas.de"&gt;Peax project&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;Roadmap Epigenomics experiment IDs:&lt;/p&gt; &lt;p&gt;E003, E004, E005, E006, E007, E008, E011, E014, E015, E016, E017, E019, E020, E026, E038, E047, E049, E062, E063, E066, E067, E068, E069, E072, E073, E074, E075, E076, E087, E101, E102, E103, E108, E111, E114, E115, E116, E117, E118, E119, E120, E121, E122, E123, E124, E125, E126, E127, E128&lt;/p&gt; &lt;p&gt;ENCODE access numbers:&lt;/p&gt; &lt;p&gt;ENCSR000EQB (2), ENCSR316UDN (1), ENCSR317SIH (1), ENCSR000EJO (1), ENCSR038XTK (1), ENCSR158VAT (1), ENCSR680SDS (1), ENCSR440FZS (1), ENCSR678PDD (1), ENCSR299INS (1), ENCSR000ENZ (1), ENCSR121ZSL (1), ENCSR796SJV (1), ENCSR035QHH (1), ENCSR515EWI (2), ENCSR000EQD (1), ENCSR271QSV (1), ENCSR426IEA (1), ENCSR000EPG (2), ENCSR000EIY (1), ENCSR595CSH (1), ENCSR000EQJ (1), ENCSR383BLX (1), ENCSR628IRM (1), ENCSR477RTP (1), ENCSR512CWR (1), ENCSR000EQI (1), ENCSR945RWN (1), ENCSR272RQX (1), ENCSR814KRX (1), ENCSR548MMD (1), ENCSR141VGA (1), ENCSR645GJD (1), ENCSR594NOE (1), ENCSR691MQJ (2), ENCSR000EPI (1), ENCSR381PXW (1), ENCSR468ZXN (1), ENCSR000EPE (2), ENCSR434OBM (1), ENCSR931UQB (1), ENCSR217RVH (1), ENCSR325LYJ (1), ENCSR004SUL (1), ENCSR035RVH (1), ENCSR217TAW (1), ENCSR184LMY (1), ENCSR940NLN (1), ENCSR000FFJ (1), ENCSR153LHP (1), ENCSR383SNM (1), ENCSR052AWE (1), ENCSR672EWY (2), ENCSR098PTC (2), ENCSR452DCM (1), ENCSR265TEK (1), ENCSR852TRT (1), ENCSR120LVW (1), ENCSR251UPG (1), ENCSR564JUY (1), ENCSR782XFY (1), ENCSR774RCO (1), ENCSR405TXU (1), ENCSR154ZNQ (1), ENCSR257BGZ (1), ENCSR148VUP (1), ENCSR593LTJ (1), ENCSR622TWS (1), ENCSR649KBB (1), ENCSR000ELO (1), ENCSR696TPW (1), ENCSR191EII (1), ENCSR019JDO (1), ENCSR000EML (1), ENCSR458LIB (2), ENCSR269SIA (2), ENCSR000EMR (1), ENCSR385AMY (1), ENCSR208DMX (1), ENCSR033STL (1), ENCSR683QJJ (1), ENCSR845CFB (1), ENCSR228VNQ (2), ENCSR517NHP (1), ENCSR337IRF (1), ENCSR000EPK (2), ENCSR554WUJ (1), ENCSR770DEN (1), ENCSR724CND (1), ENCSR911LTI (1), ENCSR857AEB (1), ENCSR959ZXU (1), ENCSR000EPD (1), ENCSR714DIF (1), ENCSR141NSQ (1), ENCSR083STA (1), ENCSR346IHH (1), ENCSR164WOF (1), ENCSR224FOA (2), ENCSR000EJQ (1), ENCSR621ENC (1), ENCSR228IKB (1), ENCSR954AJK (1), ENCSR206FSY (1), ENCSR275ICP (1), ENCSR552XJI (1), ENCSR445XYW (1), ENCSR166KPV (1), ENCSR935EVZ (1), ENCSR236SFP (1), ENCSR792ZXA (1), ENCSR426TPQ (1), ENCSR582IPV (2), ENCSR524OCB (1), ENCSR000EMV (1), ENCSR902XFY (1), ENCSR000EIS (1), ENCSR921NMD (1), ENCSR873ANE (1), ENCSR850YHJ (1)&lt;/p&gt; &lt;p&gt;In paratheses are the replicate IDs.&lt;/p&gt;</dct:description>
    <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/>
    <dct:accessRights>
      <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess">
        <rdfs:label>Open Access</rdfs:label>
      </dct:RightsStatement>
    </dct:accessRights>
    <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.5281/zenodo.2609763</dcat:accessURL>
        <dcat:byteSize>125690600</dcat:byteSize>
        <dcat:downloadURL>https://zenodo.org/record/2609763/files/chip_w-120000_r-1000.h5</dcat:downloadURL>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.5281/zenodo.2609763</dcat:accessURL>
        <dcat:byteSize>125690600</dcat:byteSize>
        <dcat:downloadURL>https://zenodo.org/record/2609763/files/chip_w-12000_r-100.h5</dcat:downloadURL>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.5281/zenodo.2609763</dcat:accessURL>
        <dcat:byteSize>125690600</dcat:byteSize>
        <dcat:downloadURL>https://zenodo.org/record/2609763/files/chip_w-3000_r-25.h5</dcat:downloadURL>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.5281/zenodo.2609763</dcat:accessURL>
        <dcat:byteSize>125690600</dcat:byteSize>
        <dcat:downloadURL>https://zenodo.org/record/2609763/files/dnase_w-120000_r-1000.h5</dcat:downloadURL>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.5281/zenodo.2609763</dcat:accessURL>
        <dcat:byteSize>125690600</dcat:byteSize>
        <dcat:downloadURL>https://zenodo.org/record/2609763/files/dnase_w-12000_r-100.h5</dcat:downloadURL>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.5281/zenodo.2609763</dcat:accessURL>
        <dcat:byteSize>125690600</dcat:byteSize>
        <dcat:downloadURL>https://zenodo.org/record/2609763/files/dnase_w-3000_r-25.h5</dcat:downloadURL>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
</rdf:RDF>
231
109
views
downloads
All versions This version
Views 231231
Downloads 109109
Data volume 13.7 GB13.7 GB
Unique views 214214
Unique downloads 4646

Share

Cite as