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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

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 Roadmap Epigenetics projects targeting H3K4me1, H3K4me3, H3K27ac, H3K9ac, H3K27me3, H3K9me3, and H3K36me (see experiment IDs below). The DNase-seq autoencoders were trained on 120 experiments from the ENCODE projects (see accession numbers below).

These autoencoders were produced as part of the Peax project.

Roadmap Epigenomics experiment IDs:

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

ENCODE access numbers:

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)

In paratheses are the replicate IDs.

Files (754.1 MB)
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chip_w-120000_r-1000.h5
md5:ad07e8759bb5aed585171cfc1994bf69
125.7 MB Download
chip_w-12000_r-100.h5
md5:18097c07e61141254115991bf6259743
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chip_w-3000_r-25.h5
md5:8dbf5a7f7d3064eb4891d217eab45552
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dnase_w-120000_r-1000.h5
md5:397ee368a676b97117bdd4c83290627f
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dnase_w-12000_r-100.h5
md5:3a464a0f820bd969b479920f049fe677
125.7 MB Download
dnase_w-3000_r-25.h5
md5:3c180c3ce233eb1e552fed724d57109f
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