title: NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes.
abstract: Transcripts in all eukaryotes are characterized by the 5'-end specific cap structure in mRNAs. Cap Analysis Gene Expression or CAGE makes use of these caps to specifically obtain cDNA fragments from the 5'-end of RNA and sequences those at high throughput for transcript identification and genome-wide mapping of transcription start sites for coding and noncoding genes. Here, we provide an improved version of our nanoCAGE protocol that has been developed for preparing CAGE libraries from as little as 50 ng of total RNA within three standard working days. Key steps in library preparation have been improved over our previously published protocol to obtain libraries having a good 5'-end selection and a more equal size distribution for higher sequencing efficiency on Illumina MiSeq and HiSeq sequencers. We recommend nanoCAGE as the method of choice for transcriptome profiling projects even from limited amounts of RNA, and as the best approach for genome-wide mapping of transcription start sites within promoter regions.
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Poulain
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
authors.forename: Sachi
authors.initials: S
authors.lastname: Kato
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
authors.forename: Ophélie
authors.initials: O
authors.lastname: Arnaud
authors.affiliation: RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.|Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Av. da Abolição, 3207-Meireles, Fortaleza, CE, 60165-081, Brazil.
authors.forename: Jean-Étienne
authors.initials: JÉ
authors.lastname: Morlighem
authors.affiliation: RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.|DNAFORM, Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0046, Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Suzuki
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. plessy@riken.jp.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. plessy@riken.jp.
authors.forename: Charles
authors.initials: C
authors.lastname: Plessy
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. matthias.harbers@riken.jp.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. matthias.harbers@riken.jp.
authors.forename: Matthias
authors.initials: M
authors.lastname: Harbers
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D011401:Promoter Regions, Genetic; D012315:RNA Caps; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D012984:Software; D024363:Transcription Initiation Site; D059467:Transcriptome
chemical_list: D012315:RNA Caps; D012333:RNA, Messenger; D022661:RNA, Untranslated
keywords: CAGE; CAGEscan; Cap analysis gene expression; Expression profiling; Multiplexing; RNA; TSS; Tagmentation; Template switching; Transcription Start Sites; UMI; Unique molecular identifiers; nanoCAGE