Other Open Access
Lekschas, Fritz;
Peterson, Brant;
Haehn, Daniel;
Ma, Eric;
Gehlenborg, Nils;
Pfister, Hanspeter
<?xml version='1.0' encoding='UTF-8'?> <record xmlns="http://www.loc.gov/MARC21/slim"> <leader>00000nam##2200000uu#4500</leader> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">Autoencoder</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">CNN</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">DNase-seq</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">ChIP-seq</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">histone mark ChIP-seq</subfield> </datafield> <controlfield tag="005">20190410032824.0</controlfield> <controlfield tag="001">2609763</controlfield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Novartis Institutes for BioMedical Research</subfield> <subfield code="a">Peterson, Brant</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Harvard University</subfield> <subfield code="0">(orcid)0000-0001-9144-3461</subfield> <subfield code="a">Haehn, Daniel</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Novartis Institutes for BioMedical Research</subfield> <subfield code="0">(orcid)0000-0003-0041-5989</subfield> <subfield code="a">Ma, Eric</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Harvard Medical School</subfield> <subfield code="0">(orcid)0000-0003-0327-8297</subfield> <subfield code="a">Gehlenborg, Nils</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Harvard University</subfield> <subfield code="0">(orcid)0000-0002-3620-2582</subfield> <subfield code="a">Pfister, Hanspeter</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">125690600</subfield> <subfield code="z">md5:ad07e8759bb5aed585171cfc1994bf69</subfield> <subfield code="u">https://zenodo.org/record/2609763/files/chip_w-120000_r-1000.h5</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">125690600</subfield> <subfield code="z">md5:18097c07e61141254115991bf6259743</subfield> <subfield code="u">https://zenodo.org/record/2609763/files/chip_w-12000_r-100.h5</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">125690600</subfield> <subfield code="z">md5:8dbf5a7f7d3064eb4891d217eab45552</subfield> <subfield code="u">https://zenodo.org/record/2609763/files/chip_w-3000_r-25.h5</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">125690600</subfield> <subfield code="z">md5:397ee368a676b97117bdd4c83290627f</subfield> <subfield code="u">https://zenodo.org/record/2609763/files/dnase_w-120000_r-1000.h5</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">125690600</subfield> <subfield code="z">md5:3a464a0f820bd969b479920f049fe677</subfield> <subfield code="u">https://zenodo.org/record/2609763/files/dnase_w-12000_r-100.h5</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">125690600</subfield> <subfield code="z">md5:3c180c3ce233eb1e552fed724d57109f</subfield> <subfield code="u">https://zenodo.org/record/2609763/files/dnase_w-3000_r-25.h5</subfield> </datafield> <datafield tag="542" ind1=" " ind2=" "> <subfield code="l">open</subfield> </datafield> <datafield tag="260" ind1=" " ind2=" "> <subfield code="c">2019-03-26</subfield> </datafield> <datafield tag="909" ind1="C" ind2="O"> <subfield code="o">oai:zenodo.org:2609763</subfield> </datafield> <datafield tag="100" ind1=" " ind2=" "> <subfield code="u">Harvard University</subfield> <subfield code="0">(orcid)0000-0001-8432-4835</subfield> <subfield code="a">Lekschas, Fritz</subfield> </datafield> <datafield tag="245" ind1=" " ind2=" "> <subfield code="a">DNase-seq and histone mark ChIP-seq convolutional autoencoders</subfield> </datafield> <datafield tag="540" ind1=" " ind2=" "> <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield> <subfield code="a">Creative Commons Attribution 4.0 International</subfield> </datafield> <datafield tag="650" ind1="1" ind2="7"> <subfield code="a">cc-by</subfield> <subfield code="2">opendefinition.org</subfield> </datafield> <datafield tag="520" ind1=" " ind2=" "> <subfield code="a"><p>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 <a href="http://www.roadmapepigenomics.org">Roadmap Epigenetics</a> projects targeting&nbsp;H3K4me1, H3K4me3, H3K27ac, H3K9ac, H3K27me3, H3K9me3, and H3K36me (see experiment IDs below). The DNase-seq autoencoders were trained on 120 experiments from the <a href="https://www.encodeproject.org">ENCODE projects</a>&nbsp;(see accession numbers below).</p> <p>These autoencoders were produced as part of the <a href="http://peax.lekschas.de">Peax project</a>.</p> <p>Roadmap Epigenomics experiment IDs:</p> <p>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</p> <p>ENCODE access numbers:</p> <p>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)</p> <p>In paratheses are the replicate IDs.</p></subfield> </datafield> <datafield tag="773" ind1=" " ind2=" "> <subfield code="n">doi</subfield> <subfield code="i">isSupplementTo</subfield> <subfield code="a">10.1101/597518</subfield> </datafield> <datafield tag="773" ind1=" " ind2=" "> <subfield code="n">doi</subfield> <subfield code="i">isVersionOf</subfield> <subfield code="a">10.5281/zenodo.2609762</subfield> </datafield> <datafield tag="024" ind1=" " ind2=" "> <subfield code="a">10.5281/zenodo.2609763</subfield> <subfield code="2">doi</subfield> </datafield> <datafield tag="980" ind1=" " ind2=" "> <subfield code="a">other</subfield> </datafield> </record>
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