LOCUS AKAAB0000000 mRNA linear ROD 17-APR-2009 DEFINITION Mus musculus 5'cDNA fragments, Oligo dT primer derived vector not used sequenced by 454 RIKEN Cap Analysis Gene Expression (CAGE) library. ACCESSION AKAAB0000000 VERSION AKAAB0000000.1 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., Hori,F., Kojima,M., Murata,M., Nishiyori,H., Sano,H., Tagami,M. and Hayashizaki,Y. TITLE Direct Submission JOURNAL Submitted (19-MAR-2009) 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 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 3 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 concatemers 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-PCR), Primer2 (MmeI-PCR)). The desired 37 bp tags were purified and ligated to form concatemers, and then the concatemer were fractionated(100-350 bp) and ligated to the plasmid ZErO-2. The ligations were finally electroporated into DH10b cells (Invitrogen). Then the colonies grown on solid medium were collected and the plasmid were extracted. The concatemers in the plasmid were amplified in a PCR stem by using the two-vector specific primers (Primer3 (CAGE amplify F1) and Primer4 (CAGE amplify R1)). The 454 adaptors were ligated to the amplified concatemer. 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. These libraries were sequenced by 454 GS20. We used in-house developed algorithms for the extraction of tags. Raw sequences containing base "N" were removed before tag extraction. 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": 5'-biotin-agagagagacctcgagtaactataacggtcctaaggtagcgacctagg (5 bp) tccgacGNNNNN-3' and "Upper oligonucleotide N6": 5'-biotin-agagagagacctcgagtaactataacggtcctaaggtagcgacctagg (5 bp) tccgacNNNNNN-3' were mixed. "Lower oligonucleotide": 5'-P-gtcgga (5 bp) cctaggtcgctaccttaggaccgttatagttactcgaggtctctctct-NH2-3' Linker2: "Upper-XmaJI": 5'-P- cctaggtcaggactcttctatagtgtcacctaaagacacacacac-NH2-3' "Lower-XmaJI": 5'-gtgtgtgtgtctttaggtgacactatagaagagtcctgacctaggNN- 3' Primer1 (uni-PCR): 5'-biotin-GTGTGTGTGTCTTTAGGTGACACTA-3' Primer2 (MmeI-PCR): 5'-biotin-AGAGAGAGACCTCGAGTAACTATAA-3' Primer3 (CAGE-amplify-F1): 5'-P-CGCTCGAGCATGCATCTAG-3' Primer4 (CAGE-amplify-R1): 5'-P-GCGAATTGGGCCCTCTAG-3' Deficient library 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 Oligo dT derived" /organism="Mus musculus" /strain="C57BL/6J" /tissue_type="hippocampus" MGA AKAAB0000001-AKAAB0046921 total number of count : 172104 Header Format >[ACC#]|[submitter's identifier]|[number of sequence count]|[map]|[free text]|[db_xref1(,db_xref2,...)]| //