8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATransMap.html src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATransMap.html index ce9a6ef..608b852 100644 --- src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATransMap.html +++ src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATransMap.html @@ -1,93 +1,93 @@ <H2>Description</H2> <P> This track shows the forward (+) and reverse (-) strand transcript map of intensity scores (estimating RNA abundance) for human NB4 cell total RNA, and human placental Poly(A)+ RNA, hybridized to the Yale MAS (Maskless Array Synthesizer) ENCODE oligonucleotide microarray, transcription mapping design #1. This array has 36-mer oligonucleotide probes approximately every 36 bp (<i>i.e.</i> end-to-end) covering all the non-repetitive DNA sequence of the ENCODE regions ENm001-ENm012. See NCBI <A HREF="https://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL2105" TARGET=_blank>GEO GPL2105</A> for details of this array design. </P> <P> This transcript map is a combined signal from three biological replicates, each with at least two technical replicates. Arrays were hybridized using either the standard Nimblegen protocol or the protocol described in Bertone <em>et al</em>. (2004). The label of each subtrack in this annotation indicates the specific protocol used for that particular data set.</P> <H2>Display Conventions and Configuration</H2> <P> This annotation follows the display conventions for composite tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the <A HREF="../goldenPath/help/hgWiggleTrackHelp.html" TARGET=_blank>Graph configuration help</A> link.</P> <H2>Methods</H2> <P> A score was assigned to each oligonucleotide probe position by combining two or more technical replicates and by using a sliding window approach. Within a sliding window of 160 bp (corresponding to 5 oligos), the hybridization intensities for all replicates of each oligonucleotide probe were compared to their respective array median score. Within the window and across all the replicates, the number of probes above and below their respective median were counted. Using the sign test, a one-sided P-value was then calculated and a score defined as score=-log(<i>P-value</i>) was assigned to the oligo in the center of the window.</P> <P> Three independent biological replicates were generated and each was hybridized to at least 2 different arrays (technical replicates).</P> <H2>Verification</H2> <P> Reasonable correlation coefficients between replicates were ensured. Additionally, transcribed regions (TARs/transfrags) were called and compared between technical and biological replicates to ensure significant overlap.</P> <H2>Credits</H2> <P> These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University.</P> <H2>References</H2> <P> Bertone, P., Stolc, V., Royce, T.E., Rozowsky, J.S., Urban, A.E., Zhu, X., Rinn, J.L., Tongprasit, W., Samanta, M. <em>et al</em>. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15539566&query_hl=7" TARGET=_blank>Global identification of human transcribed sequences with genome tiling arrays</A>. <i>Science</i> <B>306</B>(5705), 2242-6 (2004).</P> <P> Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H. <em>et al</em>. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15790807&query_hl=5" TARGET=_blank>Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution</A>. <i>Science</i> <B>308</B>(5725), 1149-54 (2005).</P> <P> Kapranov, P., Cawley, S.E., Drenkow, J., Bekiranov, S., Strausberg, R.L., Fodor, S.P. and Gingeras, T.R. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11988577&query_hl=5" TARGET=_blank>Large-scale transcriptional activity in chromosomes 21 and 22</A>. <i>Science</i> <B>296</B>(5569), 916-9 (2002).</P> <P> Kluger, Y., Tuck, D.P., Chang, J.T., Nakayama, Y., Poddar, R., Kohya, N., Lian, Z., Ben Nasr, A., Halaban, H.R. <em>et al</em>. <A HREF="https://www.pnas.org/content/101/17/6508.full" TARGET=_blank>Lineage specificity of gene expression patterns</A>. <i>Proc Natl Acad Sci U S A</i> <B>101</B>(17), 6508-13 (2004).</P> <P> Rinn, J.L., Euskirchen, G., Bertone, P., Martone, R., Luscombe, N.M., Hartman, S., Harrison, P.M., Nelson, F.K., Miller, P. <em>et al.</em> -<A HREF="http://genesdev.cshlp.org/content/17/4/529.full" +<A HREF="https://genesdev.cshlp.org/content/17/4/529.full" TARGET=_blank>The transcriptional activity of human Chromosome 22</A>. <i>Genes Dev</i> <B>17</B>(4), 529-40 (2003).</P>