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Mech."},{"key":"key\n\t\t\t\t2019022003101854900_ref65","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1016\/0092-8674(94)90522-3","article-title":"HNF-3 beta is essential for node and notochord formation in mouse development","volume":"78","author":"Ang","year":"1994","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019022003101854900_ref66","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/383407a0","article-title":"Cyclopia and defective axial patterning in mice lacking Sonic hedgehog gene function","volume":"383","author":"Chiang","year":"1996","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019022003101854900_ref67","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1016\/S0002-9440(10)61747-6","article-title":"Anorectal malformations caused by defects in sonic hedgehog signaling","volume":"159","author":"Mo","year":"2001","journal-title":"Am. J. Pathol."},{"key":"key\n\t\t\t\t2019022003101854900_ref68","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/S0022-3468(00)90014-9","article-title":"New mouse models of congenital anorectal malformations","volume":"35","author":"Kimmel","year":"2000","journal-title":"J. Pediatr. Surg."},{"key":"key\n\t\t\t\t2019022003101854900_ref69","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1053\/jpsu.2001.20722","article-title":"Murine models of VACTERL syndrome: role of sonic hedgehog signaling pathway","volume":"36","author":"Kim","year":"2001","journal-title":"J. Pediatr. Surg."},{"key":"key\n\t\t\t\t2019022003101854900_ref70","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1242\/dmm.014530","article-title":"Defining the molecular pathologies in cloaca malformation: similarities between mouse and human","volume":"7","author":"Runck","year":"2014","journal-title":"Dis. Model. Mech."},{"key":"key\n\t\t\t\t2019022003101854900_ref71","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/j.mod.2012.07.003","article-title":"Sonic hedgehog in the notochord is sufficient for patterning of the intervertebral discs","volume":"129","author":"Choi","year":"2012","journal-title":"Mech. Dev."},{"key":"key\n\t\t\t\t2019022003101854900_ref72","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0055528","article-title":"Foxa1 and Foxa2 are required for formation of the intervertebral discs","volume":"8","author":"Maier","year":"2013","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019022003101854900_ref73","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1101\/gr.177881.114","article-title":"Tn5 transposase and tagmentation procedures for massively scaled sequencing projects","volume":"24","author":"Picelli","year":"2014","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019022003101854900_ref74","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019022003101854900_ref75","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019022003101854900_ref76","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t2019022003101854900_ref77","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","article-title":"BigWig and BigBed: enabling browsing of large distributed datasets","volume":"26","author":"Kent","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019022003101854900_ref78","doi-asserted-by":"crossref","first-page":"11.12.1","DOI":"10.1002\/0471250953.bi1112s47","article-title":"BEDTools: the Swiss-army tool for genome feature analysis","volume":"47","author":"Quinlan","year":"2014","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"key\n\t\t\t\t2019022003101854900_ref79","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baw093","article-title":"The Ensembl gene annotation system","volume":"2016","author":"Aken","year":"2016","journal-title":"Database"},{"key":"key\n\t\t\t\t2019022003101854900_ref80","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nature11233","article-title":"Landscape of transcription in human cells","volume":"489","author":"Djebali","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019022003101854900_ref81","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/s12859-015-0670-5","article-title":"QoRTs: a comprehensive toolset for quality control and data processing of RNA-seq experiments","volume":"16","author":"Hartley","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t2019022003101854900_ref82","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1093\/bioinformatics\/btv694","article-title":"RNA-enrich: a cut-off free functional enrichment testing method for RNA-seq with improved detection power","volume":"32","author":"Lee","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019022003101854900_ref83","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1101\/gr.136184.111","article-title":"ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia","volume":"22","author":"Landt","year":"2012","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t2019022003101854900_ref84","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1038\/nbt.1508","article-title":"Design and analysis of ChIP-seq experiments for DNA-binding proteins","volume":"26","author":"Kharchenko","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t2019022003101854900_ref85","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12864-015-1245-6","article-title":"Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution","volume":"16","author":"Denas","year":"2015","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t2019022003101854900_ref86","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1093\/hmg\/ddi011","article-title":"Urogenital and caudal dysgenesis in adrenocortical dysplasia (ACD) mice is caused by a splicing mutation in a novel telomeric regulator","volume":"14","author":"Keegan","year":"2005","journal-title":"Hum. Mol. Genet."},{"key":"key\n\t\t\t\t2019022003101854900_ref87","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/j.ydbio.2009.07.038","article-title":"Caudal regression in adrenocortical dysplasia (ACD) mice is caused by telomere dysfunction with subsequent p53-dependent apoptosis","volume":"334","author":"Vlangos","year":"2009","journal-title":"Dev. Biol."},{"key":"key\n\t\t\t\t2019022003101854900_ref88","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.cell.2004.07.024","article-title":"Evidence for an expansion-based temporal Shh gradient in specifying vertebrate digit identities","volume":"118","author":"Harfe","year":"2004","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019022003101854900_ref89","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1016\/0092-8674(93)90627-3","article-title":"Sonic hedgehog, a member of a family of putative signaling molecules, is implicated in the regulation of CNS polarity","volume":"75","author":"Echelard","year":"1993","journal-title":"Cell"},{"key":"key\n\t\t\t\t2019022003101854900_ref90","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1242\/dev.149930","article-title":"Sonic hedgehog regulation of Foxf2 promotes cranial neural crest mesenchyme proliferation and is disrupted in cleft lip morphogenesis","volume":"144","author":"Everson","year":"2017","journal-title":"Development"},{"key":"key\n\t\t\t\t2019022003101854900_ref91","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1007\/s00418-011-0903-2","article-title":"Comparative analysis of Neph gene expression in mouse and chicken development","volume":"137","author":"Volker","year":"2012","journal-title":"Histochem. Cell Biol."},{"key":"key\n\t\t\t\t2019022003101854900_ref92","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1242\/dev.119.3.567","article-title":"Postimplantation expression patterns indicate a role for the mouse forkhead\/HNF-3 alpha, beta and gamma genes in determination of the definitive endoderm, chordamesoderm and neuroectoderm","volume":"119","author":"Monaghan","year":"1993","journal-title":"Development"},{"key":"key\n\t\t\t\t2019022003101854900_ref93","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1006\/geno.1994.1191","article-title":"The HNF-3 gene family of transcription factors in mice: gene structure, cDNA sequence, and mRNA distribution","volume":"20","author":"Kaestner","year":"1994","journal-title":"Genomics"},{"key":"key\n\t\t\t\t2019022003101854900_ref94","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1242\/dev.117.4.1321","article-title":"Chimeric analysis of T (Brachyury) gene function","volume":"117","author":"Wilson","year":"1993","journal-title":"Development"}],"container-title":["Human Molecular Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/hmg\/article-pdf\/28\/5\/736\/27894974\/ddy378.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,4]],"date-time":"2022-09-04T19:04:46Z","timestamp":1662318286000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/hmg\/article\/28\/5\/736\/5150477"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,31]]},"references-count":94,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2018,10,31]]},"published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/hmg\/ddy378","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/387977","asserted-by":"object"}]},"ISSN":["0964-6906","1460-2083"],"issn-type":[{"value":"0964-6906","type":"print"},{"value":"1460-2083","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3,1]]},"published":{"date-parts":[[2018,10,31]]}}}