FANTOM5 CAGE profiles of human and mouse samples.

Shuhei NoguchiTakahiro ArakawaShiro FukudaMasaaki FurunoAkira HasegawaFumi HoriSachi Ishikawa-KatoKaoru KaidaAi KaihoMutsumi Kanamori-KatayamaTsugumi KawashimaMiki KojimaAtsutaka KubosakiRi-Ichiroh ManabeMitsuyoshi MurataSayaka Nagao-SatoKenichi NakazatoNoriko NinomiyaHiromi Nishiyori-SuekiShohei NomaEri SaijyoAkiko SakaMizuho SakaiChristophe SimonNaoko SuzukiMichihira TagamiShoko WatanabeShigehiro YoshidaPeter ArnerRichard A AxtonMagda BabinaJ Kenneth BaillieTimothy C BarnettAnthony G BeckhouseAntje BlumenthalBeatrice BodegaAlessandro BonettiJames BriggsFrank BrombacherAilsa J CarlisleHans C CleversCarrie A DavisMichael DetmarTaeko DohiAlbert S B EdgeMatthias EdingerAnna EhrlundKarl EkwallMitsuhiro EndohHideki EnomotoAfsaneh EslamiMichela FagioliniLynsey FairbairnMary C Farach-CarsonGeoffrey J FaulknerCarmelo FerraiMalcolm E Fisher Lesley M ForresterRie FujitaJun-Ichi FurusawaTeunis B GeijtenbeekThomas GingerasDaniel GoldowitzSven GuhlReto GulerStefano GustincichThomas J HaMasahide HamaguchiMitsuko HaraYuki HasegawaMeenhard HerlynPeter HeutinkKelly J HitchensDavid A HumeTomokatsu IkawaYuri IshizuChieko KaiHiroshi KawamotoYuki I KawamuraJudith S KempfleTony J KennaJuha KereLevon M KhachigianToshio KitamuraSarah KleinS Peter KlinkenAlan J KnoxSoichi KojimaHaruhiko KosekiShigeo KoyasuWeonju LeeAndreas LennartssonAlan Mackay-SimNiklas MejhertYosuke MizunoHiromasa MorikawaMitsuru MorimotoKazuyo MoroKelly J MorrisHozumi MotohashiChristine L MummeryYutaka NakachiFumio NakaharaToshiyuki NakamuraYukio NakamuraTadasuke NozakiSoichi OgishimaNaganari OhkuraHiroshi OhnoMitsuhiro OhshimaMariko Okada-HatakeyamaYasushi OkazakiValerio OrlandoDmitry A OvchinnikovRobert PassierMargaret PatrikakisAna PomboSwati Pradhan-BhattXian-Yang QinMichael RehliPatrizia RizzuSugata RoyAntti SajantilaShimon SakaguchiHiroki SatoHironori SatohSuzana SavviAlka SaxenaChristian SchmidlClaudio SchneiderGundula G Schulze-TanzilAnita SchwegmannGuojun ShengJay W ShinDaisuke SugiyamaTakaaki SugiyamaKim M SummersNaoko TakahashiJun TakaiHiroshi TanakaHideki TatsukawaAndru TomoiuHiroo ToyodaMarc van de WeteringLinda M van den BergRoberto VerardoDipti VijayanChristine A WellsLouise N WinteringhamErnst WolvetangYoko YamaguchiMasayuki YamamotoChiyo Yanagi-MizuochiMisako YonedaYohei YonekuraPeter G ZhangSilvia ZucchelliImad AbugessaisaErik ArnerJayson HarshbargerAtsushi KondoTimo LassmannMarina LizioSerkan SahinThierry SengstagJessica SeverinHisashi ShimojiMasanori SuzukiHarukazu SuzukiJun KawaiNaoto KondoMasayoshi ItohCarsten O DaubTakeya Kasukawa Hideya KawajiPiero CarninciAlistair R R ForrestYoshihide Hayashizaki

Published in: Scientific data (2017)

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.