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/encodeUncFaire.html src/hg/makeDb/trackDb/human/encodeUncFaire.html index aa13892..482520a 100644 --- src/hg/makeDb/trackDb/human/encodeUncFaire.html +++ src/hg/makeDb/trackDb/human/encodeUncFaire.html @@ -1,87 +1,87 @@ <H2>Description</H2> <P> Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) is a procedure used to isolate chromatin that is resistant to the formation of protein-DNA cross-links. These tracks display FAIRE data from 2091 fibroblast cells hybridized to high-resolution <A HREF="https://sequencing.roche.com/en/products-solutions/by-category/target-enrichment/hybridization.html" TARGET=_blank>NimbleGen</A> arrays that tile the ENCODE regions. The four datasets, in practical terms, can be thought of as independent replicates. However, because they were part of a series of experiments aimed at optimizing cross-linking conditions in human cells, the data represent different cross-linking times (1, 2, 4, and 7 minutes). Although the individual replicates are not displayed, the replicate data and also the signal averages and the peaks for the averages can be <A TARGET=BLANK HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg17/encode/datafiles/UncFaire">downloaded</A>.</P> <H2>Display Conventions and Configuration</H2> <P> The FAIRE data are represented by three subtracks. One subtrack shows the average normalized log<sub>2</sub> ratios for the tiled probes; the other two subtracks display peaks. The peaks in one set were determined using <em>PeakFinder</em> software supplied by NimbleGen. A false positive rate (FPR) was estimated for the peak set using a permutation-based method. All peaks had an FPR of < 0.01. The peaks in the other set (Apr. 2006 update) were identified by ChIPOTle, a peak-finding algorithm that uses a sliding window to identify statistically significant signals that comprise a peak. A null distribution was determined by reflecting the negative data, which is presumed to be noise, about zero and a Gaussian distribution was fitted to it. Windows were considered significant with a p-value < 1e-25, after using the Benjamini-Hochberg correction for multiple tests.</P> <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 one subtrack, uncheck the box next to the track 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. Note that the graphical configuration options are available only for the Signal subtrack; the Peaks subtracks are fixed. </P> <H2>Methods</H2> <P> To perform FAIRE, proteins were cross-linked to DNA using 1% formaldehyde solution, the complex was sheared using sonication, and a phenol/chloroform extraction was performed to remove DNA fragments crosslinked to protein. The DNA recovered in the aqueous phase was fluorescently-labeled and hybridized to a microarray along with fluorescently-labeled genomic DNA as a control. Ratios were scaled by subtracting the Tukey Bi-weight mean for the log-ratio values from each log-ratio value, as recomended by NimbleGen. Results in yeast were consistent with enrichment for nucleosome-depleted regions of the genome. Therefore, the method may have utility as a positive selection for genomic regions with properties normally detected by assays like DNAse hypersensitivity. </P> <H2>Verification</H2> <P> The data were verified using PCR with primers designed to promoters enriched with FAIRE and downstream coding regions. </P> <H2>Credits</H2> <P> Cell culture, fixing, and DNA amplification were performed by Jonghwan Kim in the <A HREF="http://microarray.icmb.utexas.edu/" TARGET=_blank>Vishy Iyer lab</A> at the University of Texas, Austin. FAIRE was done by Paul Giresi in -the <A HREF="http://www.bio.unc.edu/faculty/lieb/labpages/default.shtml" +the <A HREF="https://bio.unc.edu/faculty/lieb/labpages/default.shtml" TARGET=_blank>Jason Lieb lab</A> at the University of North Carolina at Chapel Hill. Paul Giresi of <A HREF="https://sequencing.roche.com/en/products-solutions/by-category/target-enrichment/hybridization.html" TARGET=_blank>NimbleGen</A> did the sample labeling and hybridization with the help of Mike Singer and Roland Green. Nan Jiang at NimbleGen supplied the Software used for the permutation analysis.</P> <H2>References</H2> <P> Buck, M.J., Nobel, A.B., and Lieb, J.D. <A HREF="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-11-r97" TARGET=_blank>ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data</A>. <em>Genome Biol.</em> <B>6</B>(11), R97 (2005).</P> <P> Nagy, P.L., Cleary, M.L., Brown, P.O., and Lieb, J.L. <A HREF="https://www.pnas.org/content/100/11/6364.full" TARGET=_blank>Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin</A>. <em>PNAS</em> <B>100</B>(11), 6364-9 (2003).</P>