Data Summary

Acknowledgements

We acknowledge the original publications of data sources available in FILER and the funding they received. If you use FILER in your research, please cite the FILER paper as well as the orginal publications producing the raw data and aknowledge the funding that they received.

1000 Genome phase 3

URL: https://www.internationalgenome.org/

Publications: 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393

Funding/Acknowledgements: Funding for this work was from the Wellcome Trust Core Award 090532/Z/09/Z and Senior Investigator Award 095552/Z/11/Z (P.D.), and grants WT098051 (R.D.), WT095908 and WT109497 (P.F.), WT086084/Z/08/Z and WT100956/Z/13/Z (G.M.), WT097307 (W.K.), WT0855322/Z/08/Z (R.L.), WT090770/Z/09/Z (D.K.), the Wellcome Trust Major Overseas program in Vietnam grant 089276/Z.09/Z (S.D.), the Medical Research Council UK grant G0801823 (J.L.M.), the UK Biotechnology and Biological Sciences Research Council grants BB/I02593X/1 (G.M.) and BB/I021213/1 (A.R.L.), the British Heart Foundation (C.A.A.), the Monument Trust (J.H.), the European Molecular Biology Laboratory (P.F.), the European Research Council grant 617306 (J.L.M.), the Chinese 863 Program 2012AA02A201, the National Basic Research program of China 973 program no. 2011CB809201, 2011CB809202 and 2011CB809203, Natural Science Foundation of China 31161130357, the Shenzhen Municipal Government of China grant ZYC201105170397A (J.W.), the Canadian Institutes of Health Research Operating grant 136855 and Canada Research Chair (S.G.), Banting Postdoctoral Fellowship from the Canadian Institutes of Health Research (M.K.D.), a Le Fonds de Recherche du Québec-Santé (FRQS) research fellowship (A.H.), Genome Quebec (P.A.), the Ontario Ministry of Research and Innovation – Ontario Institute for Cancer Research Investigator Award (P.A., J.S.), the Quebec Ministry of Economic Development, Innovation, and Exports grant PSR-SIIRI-195 (P.A.), the German Federal Ministry of Education and Research (BMBF) grants 0315428A and 01GS08201 (R.H.), the Max Planck Society (H.L., G.M., R.S.), BMBF-EPITREAT grant 0316190A (R.H., M.L.), the German Research Foundation (Deutsche Forschungsgemeinschaft) Emmy Noether Grant KO4037/1-1 (J.O.K.), the Beatriu de Pinos Program grants 2006 BP-A 10144 and 2009 BP-B 00274 (M.V.), the Spanish National Institute for Health Research grant PRB2 IPT13/0001-ISCIII-SGEFI/FEDER (A.O.), Ewha Womans University (C.L.), the Japan Society for the Promotion of Science Fellowship number PE13075 (N.P.), the Louis Jeantet Foundation (E.T.D.), the Marie Curie Actions Career Integration grant 303772 (C.A.), the Swiss National Science Foundation 31003A_130342 and NCCR “Frontiers in Genetics” (E.T.D.), the University of Geneva (E.T.D., T.L., G.M.), the US National Institutes of Health National Center for Biotechnology Information (S.S.) and grants U54HG3067 (E.S.L.), U54HG3273 and U01HG5211 (R.A.G.), U54HG3079 (R.K.W., E.R.M.), R01HG2898 (S.E.D.), R01HG2385 (E.E.E.), RC2HG5552 and U01HG6513 (G.T.M., G.R.A.), U01HG5214 (A.C.), U01HG5715 (C.D.B.), U01HG5718 (M.G.), U01HG5728 (Y.X.F.), U41HG7635 (R.K.W., E.E.E., P.H.S.), U41HG7497 (C.L., M.A.B., K.C., L.D., E.E.E., M.G., J.O.K., G.T.M., S.A.M., R.E.M., J.L.S., K.Y.), R01HG4960 and R01HG5701 (B.L.B.), R01HG5214 (G.A.), R01HG6855 (S.M.), R01HG7068 (R.E.M.), R01HG7644 (R.D.H.), DP2OD6514 (P.S.), DP5OD9154 (J.K.), R01CA166661 (S.E.D.), R01CA172652 (K.C.), P01GM99568 (S.R.B.), R01GM59290 (L.B.J., M.A.B.), R01GM104390 (L.B.J., M.Y.Y.), T32GM7790 (C.D.B., A.R.M.), P01GM99568 (S.R.B.), R01HL87699 and R01HL104608 (K.C.B.), T32HL94284 (J.L.R.F.), and contracts HHSN268201100040C (A.M.R.) and HHSN272201000025C (P.S.), Harvard Medical School Eleanor and Miles Shore Fellowship (K.L.), Lundbeck Foundation Grant R170-2014-1039 (K.L.), NIJ Grant 2014-DN-BX-K089 (Y.E.), the Mary Beryl Patch Turnbull Scholar Program (K.C.B.), NSF Graduate Research Fellowship DGE-1147470 (G.D.P.), the Simons Foundation SFARI award SF51 (M.W.), and a Sloan Foundation Fellowship (R.D.H.). E.E.E. is an investigator of the Howard Hughes Medical Institute.

DASHR2

URL: https://dashr2.lisanwanglab.org/

Publications: Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS. DASHR: database of small human noncoding RNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D216-22. doi: 10.1093/nar/gkv1188 Epub 2015 Nov 8.

Kuksa PP, Amlie-Wolf A, Katanić Ž, Valladares O, Wang LS, Leung YY. DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. Bioinformatics. 2019 Mar 15;35(6):1033-1039. doi: 10.1093/bioinformatics/bty709

Funding/Acknowledgements: National Institute of General Medical Sciences [R01-GM099962]; National Institute on Aging [U54-AG052427, U01-AG032984, U24-AG041689, UF1-AG047133], National Institute on Aging [T32-AG00255].

ENCODE

URL: https://www.encodeproject.org/

Publications: Luo Y, Hitz BC, Gabdank I, Hilton JA, Kagda MS, Lam B, Myers Z, Sud P, Jou J, Lin K, Baymuradov UK, Graham K, Litton C, Miyasato SR, Strattan JS, Jolanki O, Lee JW, Tanaka FY, Adenekan P, O'Neill E, Cherry JM. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 2020 Jan 8;48(D1):D882-D889. doi: 10.1093/nar/gkz1062

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247

Funding/Acknowledgements: National Human Genome Research Institute, National Institutes of Health [U24 HG009397]. The content is solely theresponsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. The funders had no role in design, data processing, implementation, decision to publish, or preparation of the manuscript. Funding for open access charge: National Human Genome Research Institute, National Institutes of Health [U24 HG009397].

We would like to thank past and current members of the ENCODE, modENCODE, modERN, GGR and REMC consortia in addition to the staff at the NCBI Entrez Gene, HGNC, MGNC, FlyBase, WormBase, IHEC, GA4GH, 4DN, T2D AMP Consortium, UCSC Genome, ENSEMBL and Valis browsers and the many talented graduate researchers, postdocs, bioinformaticians and ENCODE portal users for countless hours of data creation, site testing and feedback, without whom the ENCODE portal website would not be possible.

ENSEMBL

URL: http://useast.ensembl.org/index.html

Publications: Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, Brooks L, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Martinez JG, Guijarro-Clarke C, Gymer A, Hardy M, Hollis Z, Hourlier T, Hunt T, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Marugán JC, Mohanan S, Mushtaq A, Naven M, Ogeh DN, Parker A, Parton A, Perry M, Piližota I, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Pérez-Silva JG, Stark W, Steed E, Sutinen K, Sukumaran R, Sumathipala D, Suner MM, Szpak M, Thormann A, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Willhoft N, Winterbottom A, Wass E, Chakiachvili M, Flint B, Frankish A, Giorgetti S, Haggerty L, Hunt SE, IIsley GR, Loveland JE, Martin FJ, Moore B, Mudge JM, Muffato M, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Dyer S, Harrison PW, Howe KL, Yates AD, Zerbino DR, Flicek P. Ensembl 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995. doi: 10.1093/nar/gkab1049

Funding/Acknowledgements: Wellcome Trust [WT108749/Z/15/Z]; National Human Genome Research Institute of the National Institutes of Health [U41HG007823, 2U41HG007234, U41HG010972, 2U24HG007497-05]; Biotechnology and Biological Sciences Research Council [BB/N019563/1, BB/M011615/1, BB/S020152/1, BB/P016855/1, BB/S02011X/1, BB/P024602/1]; Open Targets, Wellcome Trust [WT104947/Z/14/Z, WT200990/Z/16/Z, WT201535/Z/16/Z, WT108749/Z/15/A, WT212925/Z/18/Z, WT218328/B/19/Z]; British Council [414710385]; ELIXIR: the research infrastructure for life-science data, and the European Molecular Biology Laboratory; European Union's Horizon 2020 research and innovation programme [733161 (MultipleMS), 731060 (INFRAVEC2), 825575 (EJP RD), 817923 (AQUA-FAANG), 817998 (GENESWitCH), 815668 (BovReg)]; Save the Tasmanian Devil Program. Funding for open access charge: Wellcome [WT108749/Z/15/Z].

FANTOM5

URL: https://fantom.gsc.riken.jp/

Publications: Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H; FANTOM consortium. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 5;16(1):22. doi: 10.1186/s13059-014-0560-6

Lizio M, Abugessaisa I, Noguchi S, Kondo A, Hasegawa A, Hon CC, de Hoon M, Severin J, Oki S, Hayashizaki Y, Carninci P, Kasukawa T, Kawaji H. Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. Nucleic Acids Res. 2019 Jan 8;47(D1):D752-D758. doi: 10.1093/nar/gky1099

Funding/Acknowledgements: Research grants to RIKEN Center for Life Science Technologies, RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Integrative Medical Sciences from the Japan Ministry of Education, Culture, Sports, Science and Technology (MEXT); Japan Society for the Promotion of Science KAKENHI Grants [16H02902, 16K12529 to H.K.]; Research grant from National Bioscience Database Center of the Japan Science and Technology Agency. Funding for open access charge: MEXT.

FANTOM5 Enhancers

URL: https://slidebase.binf.ku.dk/

Publications: Ienasescu H, Li K, Andersson R, Vitezic M, Rennie S, Chen Y, Vitting-Seerup K, Lagoni E, Boyd M, Bornholdt J, de Hoon MJ, Kawaji H, Lassmann T; FANTOM Consortium, Hayashizaki Y, Forrest AR, Carninci P, Sandelin A. On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. Database (Oxford). 2016 Dec 26;2016:baw144. doi: 10.1093/database/baw144

Funding/Acknowledgements: This work is part of the FANTOM5 project. Data, tools and co-published manuscripts are summarized at http://fantom.gsc.riken.jp/5/. FANTOM5 was made possible by a Research Grant for RIKEN OSC from MEXT to YH, Grant from MEXT for the RIKEN PMI to YH, Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT to YH and Grant from MEXT to the RIKEN CLST.

ELIXIR, the Novo Nordisk Foundation and the Lundbeck Foundation (to A.S.).

GTEx

URL: https://gtexportal.org/home/

Publications: GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science. 2020 Sep 11;369(6509):1318-1330. doi: 10.1126/science.aaz1776

Funding/Acknowledgements: This work was supported by the Common Fund of the Office of the Director, U.S. National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, NIA, NIAID, and NINDS through NIH contracts HHSN261200800001E (Leidos Prime contract with NCI: A.M.S., D.E.T., N.V.R., J.A.M., L.S., M.E.B., L.Q., T.K., D.B., K.R., A.U.), 10XS170 (NDRI: W.F.L., J.A.T., G.K., A.M., S.S., R.H., G.Wa., M.J., M.Wa., L.E.B., C.J., J.W., B.R., M.Hu., K.M., L.A.S., H.M.G., M.Mo., L.K.B.), 10XS171 (Roswell Park Cancer Institute: B.A.F., M.T.M., E.K., B.M.G., K.D.R., J.B.), 10X172 (Science Care Inc.), 12ST1039 (IDOX), 10ST1035 (Van Andel Institute: S.D.J., D.C.R., D.R.V.), HHSN268201000029C (Broad Institute: F.A., G.G., K.G.A., A.V.S., X.Li., E.T., S.G., A.G., S.A., K.H.H., D.T.N., K.H., S.R.M., J.L.N.), 5U41HG009494 (F.A., G.G., K.G.A.), and through NIH grants R01 DA006227-17 (Univ. of Miami Brain Bank: D.C.M., D.A.D.), Supplement to University of Miami grant DA006227 (D.C.M., D.A.D.), R01 MH090941 (Univ. of Geneva), R01 MH090951 and R01 MH090937 (Univ. of Chicago), R01 MH090936 (Univ. of North Carolina-Chapel Hill), R01MH101814 (M.M-A., V.W., S.B.M., R.G., E.T.D., D.G-M., A.V.), U01HG007593 (S.B.M.), R01MH101822 (C.D.B.), U01HG007598 (M.O., B.E.S.), U01MH104393 (A.P.F.), extension H002371 to 5U41HG002371 (W.J.K) as well as other funding sources: R01MH106842 (T.L., P.M., E.F., P.J.H.), R01HL142028 (T.L., Si.Ka., P.J.H.), R01GM122924 (T.L., S.E.C.), R01MH107666 (H.K.I.), P30DK020595 (H.K.I.), UM1HG008901 (T.L.), R01GM124486 (T.L.), R01HG010067 (Y.Pa.), R01HG002585 (G.Wa., M.St.), Gordon and Betty Moore Foundation GBMF 4559 (G.Wa., M.St.), 1K99HG009916-01 (S.E.C.), R01HG006855 (Se.Ka., R.E.H.), BIO2015-70777-P, Ministerio de Economia y Competitividad and FEDER funds (M.M-A., V.W., R.G., D.G-M.), la Caixa Foundation ID 100010434 under agreement LCF/BQ/SO15/52260001 (D.G-M.), NIH CTSA grant UL1TR002550-01 (P.M.), Marie-Skłodowska Curie fellowship H2020 Grant 706636 (S.K-H.), R35HG010718 (E.R.G.), FPU15/03635, Ministerio de Educación, Cultura y Deporte (M.M-A.), R01MH109905, 1R01HG010480 (A.Ba.), Searle Scholar Program (A.Ba.), R01HG008150 (S.B.M.), 5T32HG000044-22, NHGRI Institutional Training Grant in Genome Science (N.R.G.), EU IMI program (UE7-DIRECT-115317-1) (E.T.D., A.V.), FNS funded project RNA1 (31003A_149984) (E.T.D., A.V.), DK110919 (F.H.), F32HG009987 (F.H.), Massachusetts Lions Eye Research Fund Grant (A.R.H.).

Homer

URL: http://homer.ucsd.edu/homer/index.html

Publications: Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010 May 28;38(4):576-89. doi: 10.1016/j.molcel.2010.05.004

Funding/Acknowledgements: We thank Dr. Bing Ren, Dr. Michael Rehli and Dr. Constanze Bonifer for discussions and reading of the manuscript, Dr. Gary Hardiman and especially Colleen Ludka for assistance with Solexa sequencing, Rosa Luna for technical assistance, Dr. Young-Soo Kwon for suggestions and discussions and Lynn Bautista for assistance with manuscript preparation. SH was supported by an NIH postdoctoral training grant. These studies were primarily funded by NURSA consortium grant No DK62434 and further supported by NIH grants to CKG (HC088093, DK063491, CA52599), HS (P50 GM081892-01A1) and CM and a Foundation Leducq Transatlantic Network Grant to CKG. HS is an HHMI Investigator.

Reference Genome

URL: https://www.ncbi.nlm.nih.gov/grc

Publications: Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T. Modernizing reference genome assemblies. PLoS Biol. 2011 Jul;9(7):e1001091. doi: 10.1371/journal.pbio.1001091 Epub 2011 Jul 5.

Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 2017 May;27(5):849-864. doi: 10.1101/gr.213611.116 Epub 2017 Apr 10.

Funding/Acknowledgements: This research was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine, the Wellcome Trust (grant numbers WT095908, WT098051, and WT104947/Z/14/Z), and the European Molecular Biology Laboratory. S.K. and A.M.P. were supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health. This study utilized the computational resources of the Biowulf system at the National Institutes of Health, Bethesda, MD (http://biowulf.nih.gov). Work at MGI was supported by National Institutes of Health grants 5U54HG003079 and 5U41HG007635. Work by E.E.E. was supported in part by National Institutes of Health grants HG002385 and HG007635. E.E.E. is an investigator of the Howard Hughes Medical Institute. The GRC wishes to acknowledge the invaluable assistance and contributions of the many external collaborators and the RefSeq and HAVANA annotation groups who shared data, expertise, and advice in the effort to update the reference assembly sequence. A list of genome-wide and region-specific collaborators can be found at the GRC website (https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/credits.shtml). Additionally, the GRC would like to thank Jim Knight and Stephan Schuster for submitting sequence from an RP11-based WGS assembly to INSDC (GCA_000442295.1), making it available for use in reference curation. The MGI would like to thank Susie Rock and Aye Wollam for their oversight of the assembly curation and finishing pipelines at the McDonnell Genome Institute. WTSI thanks Paul Heath, Guy Griffiths, Britt Killian, and Eduardus Zuiderwijk for their technical and computational contributions. NCBI thanks Tayebeh Rezaie-Jami, Eugene Yaschenko, Avi Kimchi, and Karen Clark for their helpful discussion and expertise in content and data management, and Chris O'Sullivan for providing the SRA and dbGaP submission statistics. EBI thanks Bronwen Aken for providing the ENA submission statistics, as well as Carlos García Girón and Amonida Zadissa. We thank Uravashi Surti for her work to develop the CHM1 and CHM13 cell lines.

ROADMAP

URL: http://www.roadmapepigenomics.org/

Publications: Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248

Funding/Acknowledgements: This work was supported by the NIH Common Fund as part of the NIH Roadmap Epigenomics Program through U01ES017155 (BB/AM), U01ES017154 (JC/MM), U01ES017166 (BR), U01ES017156 (JS), U01DA025956 (AM/AB), and by NHGRI through RC1HG005334, R01HG004037 (MK), RO1NS078839 (L-HT). This work was also supported by NIH fellowship grants F32HL110473 and K99HL119617 (S.L.), and NSF CAREER award 1254200 (J.E.). We acknowledge program leadership by members of the NIH Epigenomics Workgroup, especially John S. Satterlee, Frederick L. Tyson, Joni Rutter, Kimberly A. McAllister, Astrid Haugen, Christine Colvis (NCATS), James Battey (NIDCD), Linda Birnbaum (NIEHS), and Nora Volkow (NIDA). We acknowledge feedback from our External Scientific Panel members Marisa Bartolomei, Stephen Baylin, Stephan Beck, Aravinda Chakravarti, Laurie Jackson-Grusby, Jason Lieb, Steve Peckman, John Quackenbush, and Steve Stice. Sample procurement was supported by grants 5R24HD000836 (IAG) for staged fetal tissues; P30AG10161, R01AG15819, R01AG17917 (DAB) and U01AG46152 (PLD, DAB) for adult brain samples.

TargetScan

URL: https://www.targetscan.org/vert_72/

Publications: Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015 Aug 12;4:e05005. doi: 10.7554/eLife.05005

Funding/Acknowledgements: This paper was supported by the following grants:

1)     National Institutes of Health (NIH) GM067031 to Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel.

2)     Howard Hughes Medical Institute (HHMI) Investigator to David P Bartel.

3)     National Science Foundation (NSF) Graduate Research Fellowship to Vikram Agarwal.

FACTORBOOK

URL:

UCSC: https://genome.ucsc.edu/

Factorbook: https://www.factorbook.org/

Publications:

UCSC: Lee BT, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Muthuraman P, Nassar LR, Nguy B, Pereira T, Perez G, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kuhn RM, Haeussler M, Kent WJ. The UCSC Genome Browser database: 2022 update. Nucleic Acids Res. 2022 Jan 7;50(D1):D1115-D1122. doi: 10.1093/nar/gkab959

Factorbook: Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. doi: 10.1093/nar/gks1221 Epub 2012 Nov 29.

Funding/Acknowledgements:

UCSC: National Human Genome Research Institute [5U41HG002371 to G.P.B., A.B-P., J.C., H.C., C.F., J.N.G., M.H., A.S.H., W.J.K., R.M.K., B.T.L., C.M.L., L.R.N, G.P., B.J.R., K.R.R., D.S., M.L.S., B.D.W., A.S.Z., 5U41HG007234 to M.D., 5R01HG010329 to M.D., M.H.]; National Institutes of Health [5U01HG010971 to M.D.]; U.S. Department of Health and Human Services [1U41HG010972 to M.H.]; Howard Hughes Medical Institute [090100 to D.H.]; Silicon Valley Community Foundation [2017-171531(5022) to G.P.B., J.C., C.F., W.J.K., B.T.L., P.M., B.N., T.P., M.L.S., A.S.Z., COVID-19 Testing to H.C., M.H.]; Center for Information Technology Research in the Interest of Society [2020-0000000026 to A.S.H., L.R.N., B.J.R.]; University of California Office of the President Emergency COVID-19 Research Seed Funding [R00RG2456 to M.H., L.R.N.]; California Department of Public Health [20-11088 to M.H., A.S.H.]; California HIV/AIDS Research Program [R01RG3764 to M.H., L.R.N.]. Funding for open access charge: National Human Genome Research Institute [5U41HG002371].

Factorbook: Funding for open access charge: National Institutes of Health [U01 HG004695; and U41 HG007000].

RefSeq

URL:

UCSC:  https://genome.ucsc.edu

RefSeq: http://www.ncbi.nlm.nih.gov/refseq/

Publications:

UCSC: Lee BT, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Muthuraman P, Nassar LR, Nguy B, Pereira T, Perez G, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kuhn RM, Haeussler M, Kent WJ. The UCSC Genome Browser database: 2022 update. Nucleic Acids Res. 2022 Jan 7;50(D1):D1115-D1122. doi: 10.1093/nar/gkab959

RefSeq: Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. doi: 10.1093/nar/gkt1114 Epub 2013 Nov 19.

Funding/Acknowledgements:

UCSC: National Human Genome Research Institute [5U41HG002371 to G.P.B., A.B-P., J.C., H.C., C.F., J.N.G., M.H., A.S.H., W.J.K., R.M.K., B.T.L., C.M.L., L.R.N, G.P., B.J.R., K.R.R., D.S., M.L.S., B.D.W., A.S.Z., 5U41HG007234 to M.D., 5R01HG010329 to M.D., M.H.]; National Institutes of Health [5U01HG010971 to M.D.]; U.S. Department of Health and Human Services [1U41HG010972 to M.H.]; Howard Hughes Medical Institute [090100 to D.H.]; Silicon Valley Community Foundation [2017-171531(5022) to G.P.B., J.C., C.F., W.J.K., B.T.L., P.M., B.N., T.P., M.L.S., A.S.Z., COVID-19 Testing to H.C., M.H.]; Center for Information Technology Research in the Interest of Society [2020-0000000026 to A.S.H., L.R.N., B.J.R.]; University of California Office of the President Emergency COVID-19 Research Seed Funding [R00RG2456 to M.H., L.R.N.]; California Department of Public Health [20-11088 to M.H., A.S.H.]; California HIV/AIDS Research Program [R01RG3764 to M.H., L.R.N.]. Funding for open access charge: National Human Genome Research Institute [5U41HG002371].

RefSeq: Funding for open access charge: Intramural Research Program of the National Institutes of Health, National Library of Medicine.

REPEATS

URL:

UCSC: https://genome.ucsc.edu

Repeatmasker: http://www.repeatmasker.org/

Publications:

UCSC: Lee BT, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Muthuraman P, Nassar LR, Nguy B, Pereira T, Perez G, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kuhn RM, Haeussler M, Kent WJ. The UCSC Genome Browser database: 2022 update. Nucleic Acids Res. 2022 Jan 7;50(D1):D1115-D1122. doi: 10.1093/nar/gkab959

Repbase: Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110(1-4):462-7. doi: 10.1159/000084979

Funding/Acknowledgements:

UCSC: National Human Genome Research Institute [5U41HG002371 to G.P.B., A.B-P., J.C., H.C., C.F., J.N.G., M.H., A.S.H., W.J.K., R.M.K., B.T.L., C.M.L., L.R.N, G.P., B.J.R., K.R.R., D.S., M.L.S., B.D.W., A.S.Z., 5U41HG007234 to M.D., 5R01HG010329 to M.D., M.H.]; National Institutes of Health [5U01HG010971 to M.D.]; U.S. Department of Health and Human Services [1U41HG010972 to M.H.]; Howard Hughes Medical Institute [090100 to D.H.]; Silicon Valley Community Foundation [2017-171531(5022) to G.P.B., J.C., C.F., W.J.K., B.T.L., P.M., B.N., T.P., M.L.S., A.S.Z., COVID-19 Testing to H.C., M.H.]; Center for Information Technology Research in the Interest of Society [2020-0000000026 to A.S.H., L.R.N., B.J.R.]; University of California Office of the President Emergency COVID-19 Research Seed Funding [R00RG2456 to M.H., L.R.N.]; California Department of Public Health [20-11088 to M.H., A.S.H.]; California HIV/AIDS Research Program [R01RG3764 to M.H., L.R.N.]. Funding for open access charge: National Human Genome Research Institute [5U41HG002371].