LOCUS AFAAQ0000000 mRNA linear HUM 17-APR-2009 DEFINITION Homo sapiens 5'cDNA fragments, random primer derived 1 year infant peripheral blood THP-1 cultured 24 hours after PMA experimental_name:RIKEN_cell_6th,rna_batch_name:LOT-No.7 RIKEN Cap Analysis Gene Expression (CAGE) library. ACCESSION AFAAQ0000000 VERSION AFAAQ0000000.1 KEYWORDS MGA; 5'-end tag; CAGE (Cap Analysis Gene Expression). SOURCE Homo sapiens ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. REFERENCE 1 AUTHORS Arakawa,T., Carninci,P., Forrest,A.R.R., Fukuda,S., Hasegawa,A., Hasegawa,Y., Hirakiyama,A., Hori,F., Kaiho,A., Kanamori-Katayama,M., Kawai,J., Kawashima,T., Kawazu,C., Kojima,M., Kubosaki,A., Maeda,N., Murakami,K., Murata,M., Nishiyori,H., Sakaba,C., Sano,H., Suzuki,H., Tagami,M., Takahashi,Y. and Hayashizaki,Y. TITLE Direct Submission JOURNAL Submitted (28-MAR-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 CONSRTM The FANTOM Consortium and the Riken Omics Science Center TITLE The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line JOURNAL Nat. Genet., 10.1038/ng.375 (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 REFERENCE 4 AUTHORS Shiraki,T., Kondo,S., Katayama,S., Waki,K., Kasukawa,T., Kawaji,H., Kodzius,R., Watahiki,A., Nakamura,M., Arakawa,T., Fukuda,S., Sasaki,D., Podhajska,A., Harbers,M., Kawai,J., Carninci,P. and Hayashizaki,Y. TITLE Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage JOURNAL Proc. Natl. Acad. Sci. U.S.A. 100, 15776-15781 (2003) COMMENT CAGE library was prepared and sequenced in Genome Science Laboratory (Wako) and Genome Exploration Research Group Genomics Science Center (GSC) : (Present) Omics Science Center in RIKEN Yokohama Institute 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' Tissues were provided by Dr. David Hume (University of Edinburgh, The Roslin Institute and Royal (Dick) School of Veterinary Studies), whose assistance we gratefully acknowledge. FEATURES Location/Qualifiers source /cell_line="THP-1" /clone_lib="human Cap Analysis Gene Expression (CAGE) library" /culture_collection="ATCC:TIB-202" /db_xref="taxon:9606" /dev_stage="1 year infant" /mol_type="mRNA" /note="primer random derived" /note="condition: cultured 24 hours after PMA" /note="comment: experimental_name:RIKEN_cell_6th, rna_batch_name:LOT-No.7" /organism="Homo sapiens" /sex="male" /tissue_type="peripheral blood" MGA AFAAQ0000001-AFAAQ0546880 total number of count : 1346653 Header Format >[ACC#]|[submitter's identifier]|[number of sequence count]|[map]|[free text]|[db_xref1(,db_xref2,...)]| //