38aed9a87ffb6dfe6550f81318e4989c209ec0d1 jnavarr5 Tue Apr 30 09:29:58 2019 -0700 Updating http to https for mm7, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/mouse/rikenCageTc.html src/hg/makeDb/trackDb/mouse/rikenCageTc.html index 7f6ba9b..7373706 100644 --- src/hg/makeDb/trackDb/mouse/rikenCageTc.html +++ src/hg/makeDb/trackDb/mouse/rikenCageTc.html @@ -1,112 +1,112 @@ <H2>Description</H2> <P> This track shows transcription start points as defined by the regions of CAGE (5' Cap Analysis Gene Expression) tag clusters. CAGE tags are 19-20-mers sequenced from 5' ends of full-length cDNAs produced using RIKEN full-length cDNA technology. A CAGE cluster is defined as one or more overlapping CAGE tags on the same strand, regardless of tissue of origin. The full annotation of a cluster, including tissue(s) of origin, can be obtained from the <A HREF="http://fantom31p.gsc.riken.jp/cage_analysis/mm5/" TARGET=_blank>CAGE Analysis Viewer</A>, via a link on the details page for that cluster. <H2>Methods</H2> <P> The CAGE tags are sequenced from the 5' ends of full-length cDNAs produced using RIKEN full-length cDNA technology. To create the tag, a linker was attached to the 5' end of full-length cDNAs which had been selected by cap trapping. The first 20 bp of the cDNA were cleaved using the class II restriction enzyme, MmeI, followed by PCR amplification. Concatamers of the resulting 32 bp tags were then formed for more efficient sequencing. For more information on CAGE, see Shiraki <em>et al.</em> (2003) and Carninci <EM>et al</EM> (2005). <A HREF="http://genome.gsc.riken.go.jp/home.html" TARGET=_blank>RIKEN</A> website for information about RIKEN full-length cDNA technologies. The mapping methodology employed in this annotation will be described in upcoming publications.</P> <H2>Credits</H2> <P> These data were contributed by the Functional Annotation of Mouse (<A HREF="http://fantom.gsc.riken.jp/" TARGET=_blank>FANTOM</A>) Consortium, RIKEN Genome Science Laboratory and <A HREF="http://genome.gsc.riken.jp/home.html" TARGET=_blank> RIKEN Genome Exploration Research Group</A> (Genome Network Project Core Group). </P> <P> <B>FANTOM Consortium:</B> P. Carninci, T. Kasukawa, S. Katayama, Gough, M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, V. Harokopos, Y. Hayashi, S. Henning, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. T. Krishnan, A.F. Kruger, K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, W. Qu, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. Salzberg, A. Sandelin, C. Schneider, C. Schoenbach, K. Sekiguchi, C. A. M. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegene, R. Verardo, C. L. Wei, K. Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. Wahlestedt, J. Mattick, D. Hume. </P> <P> <B>RIKEN Genome Exploration Research Group:</B> C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai. </P> <P> <B>General Organizer</B>: Y. Hayashizaki <H2>References</H2> <p> Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C <em>et al</em>. -<a href="http://science.sciencemag.org/content/309/5740/1559" target="_blank"> +<a href="https://science.sciencemag.org/content/309/5740/1559" target="_blank"> The transcriptional landscape of the mammalian genome</a>. <em>Science</em>. 2005 Sep 2;309(5740):1559-63. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16141072" target="_blank">16141072</a> </p> <p> Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T <em>et al</em>. -<a href="http://www.pnas.org/content/100/26/15776" target="_blank"> +<a href="https://www.pnas.org/content/100/26/15776" target="_blank"> Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage</a>. <em>Proc Natl Acad Sci U S A</em>. 2003 Dec 23;100(26):15776-81. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14663149" target="_blank">14663149</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC307644/" target="_blank">PMC307644</a> </p>