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DNase-seq and histone mark ChIP-seq convolutional autoencoders

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

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    <subfield code="a">&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;

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March 26, 2019
DOI:
10.5281/zenodo.2609763

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Keyword(s):
Autoencoder CNN DNase-seq ChIP-seq histone mark ChIP-seq
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