LOCUS AGAAA0000000 mRNA linear ROD 17-APR-2009 DEFINITION Mus musculus 5'cDNA fragments, random primer derived adult hippocampus RIKEN Cap Analysis Gene Expression (CAGE) library. ACCESSION AGAAA0000000 VERSION AGAAA0000000.1 KEYWORDS MGA; 5'-end tag; CAGE (Cap Analysis Gene Expression). SOURCE Mus musculus ORGANISM Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus. REFERENCE 1 AUTHORS Arakawa,T., Carninci,P., Fukuda,S., Hasegawa,A., Hayashida,Y., Hori,F., Kojima,M., Maeda,N., Murata,M., Nishiyori,H., Sano,H., Tagami,M. and Hayashizaki,Y. TITLE Direct Submission JOURNAL Submitted (17-JUN-2008) to the DDBJ/EMBL/GenBank databases. Contact:Yoshihide Hayashizaki The Institute of Physical and Chemical Research (RIKEN), Omics Science Center, RIKEN Yokohama Institute; 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan URL :http://www.osc.riken.jp/ REFERENCE 2 AUTHORS Valen,E., Pascarella,G., Chalk,A., Maeda,N., Kojima,M., Kawazu,C., Murata,M., Nishiyori,H., Lazarevic,D., Motti,D., Marstrand,T.T., Tang,M.E., Zhao,X., Krogh,A., Winther,O., Arakawa,T., Kawai,J., Wells,C., Daub,C., Harbers,M., Hayashizaki,Y., Gustincich,S., Sandelin,A. and Carninci,P. TITLE Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE JOURNAL Genome Res. 19, 255-265 (2009) REMARK Publication_Status: Available-Online REFERENCE 3 AUTHORS Faulkner,G.J., Kimura,Y., Daub,C.O., Wani,S., Plessy,C., Irvine,K.M., Schroder,K., Cloonan,N., Steptoe,A.L., Lassmann,T., Waki,K., Hornig,N., Arakawa,T., Takahashi,H., Kawai,J., Forrest,A.R.R., Suzuki,H., Hayashizaki,Y., Hume,D.A., Orlando,V., Grimmond,S.M. and Carninci,P. TITLE The regulated retrotransposon transcriptome of mammalian cells JOURNAL Nat. Genet., 10.1038/ng.368 (2009) In press REMARK Publication_Status: Available-Online REFERENCE 4 AUTHORS Kawaji,H., Severin,J., Lizio,M., Waterhouse,A., Katayama,S., Irvine,K.M., Hume,D.A., Forrest,A.R.R., Suzuki,H., Carninci,C., Hayashizaki,Y. and Daub,C.O. TITLE The FANTOM Web Resource: from mammalian transcriptional landscape to its dynamic regulation JOURNAL Genome Biol. (2009) In press COMMENT Please visit our web site for further details. URL:http://www.osc.riken.jp/ The CAGE (cap analysis gene expression) tags are obtained by sequencing concatamers of DNA tags deriving from the initial 20/21 nucleotides from 5' end mRNAs, prepared in accordance to Shiraki et al. (Proc Natl Acad Sci U S A. 100, 15776-81, 2003). At first step, full-length cDNAs were selected with the Cap-Trapper. Next, a specific linker (Linker1, which contains the ClassIIs restriction enzyme site MmeI) was ligated to the cDNA. Linker1 may contain extra 5 bp sequences tag, and 15 of such different sequences tags were used to tag different starting RNA samples. Then the second strand of cDNA synthesized. Resulting double-stranded cDNAs were cleaved by the restriction enzyme MmeI and a second linker (Linker2) was ligated to the 2 bp overhang at the MmeI cleaved site, to produce a 5' 20/21 tag having two linkers at both sides. The ligation products were separated from unmodified DNA with magnetic beads. The 5' end cDNA tags were released from the beads, and the DNA fragments were amplified in a PCR step by using the two linker-specific primers (Primer1 (uni-short-PCR), Primer2 (MmeI-short-PCR)). The desired 32-37 bp tags were purified and ligated to form concatemers by adding 454 adaptors A/B (1/20 amount of tags) to tags as described in the original publication (Nature. 437,376-80,2005). The sample was purified with GFX column to eliminate short concatemers. Then the library was sequenced with Genome Sequencer FLX System. Each CAGE tag comprises short sequences of about 20 bp derived from the 5' end of a full-length cDNA. The length of a CAGE tag may vary due to the limited specificity of MmeI. Note that up to 70% of the CAGE tags may have an unspecific G in the first position at the 5' end. We used in-house developed algorithms for the extraction of tags. CAGE tags were extracted with the exact full match to linker sequences and tag length is allowed between 18-24 bp. Linker1: "Upper oligonucleotide GN6": biotin-agagagagacctcgagtaactataacggtcctaaggtagcgacctagg (5 bp) tccgacGNNNNN and "Upper oligonucleotide N6": biotin-agagagagacctcgagtaactataacggtcctaaggtagcgacctagg (5 bp) tccgacNNNNNN were mixed. "Lower oligonucleotide": phosphate group-gtcgga (5 bp) cctaggtcgctaccttaggaccgttatagttactcgaggtctctctc t-NH2 Linker2: "Upper-XmaJI": Pi-cctaggtcaggactcttctatagtgtcacctaaagacaca cacac -NH2 "Lower-XmaJI": gtgtgtgtgtctttaggtgacactatagaagagtcctgacc taggNN Primer1 (uni-short-PCR): 5'-biotin-GGTGACACTATAGAAGAGTCCTG-3' Primer2 (MmeI-short-PCR): 5'-biotin-CGGTCCTAAGGTAGCGACCTAG-3' FEATURES Location/Qualifiers source /clone_lib="mouse Cap Analysis Gene Expression (CAGE) library" /db_xref="taxon:10090" /dev_stage="adult" /mol_type="mRNA" /note="primer random derived" /organism="Mus musculus" /sex="male" /strain="C57BL/6J" /tissue_type="hippocampus" MGA AGAAA0000001-AGAAA0552486 total number of count : 1942393 Header Format >[ACC#]|[submitter's identifier]|[number of sequence count]|[map]|[free text]|[db_xref1(,db_xref2,...)]| //