198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html index f7d8244e5a8..a4ffb6431de 100644 --- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html +++ src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html @@ -1,152 +1,152 @@ <H2>Description</H2> <P>This track shows probable binding sites of the specified transcription factors (TFs) in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for TF binding (<I>Signal</I>), along with sites that have the greatest evidence of transcription factor binding, as identified by the PeakSeq algorithm (<I>Peaks</I>). <P> The sequence reads, quality scores, and alignment coordinates from these experiments are available for download. </P> <H2>Display Conventions and Configuration</H2> <P> This track is a multi-view composite track that contains multiple data types (<EM>views</EM>). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>. This track contains the following views: <DL> <DT><I>Peaks</I></DT><DD> Regions of signal enrichment based on processed data (normalized data from pooled replicates). Intensity is represented in grayscale, the darker shading shows higher intensity (a solid vertical line -in the peak region represents the the point with the highest signal). +in the peak region represents the point with the highest signal). ENCODE Peaks tables contain fields for statistical significance, including FDR (<a href="/goldenPath/help/qValue.html" target="_blank">qValue</a>).</DD> <DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on processed data.</DD> </DL> <H2>Methods</H2> <P> Cells were grown according to the approved <a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>. For details on the chromatin immunoprecipitation protocol used, see Euskirchen <EM>et. al.</EM>, (2007), Rozowsky <EM>et. al.</EM> (2009) and Auerbach <EM>et. al.</EM> (2009). </P> <P> DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags, a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome. Reads were pooled from all submitted replicates to generate the Peak and Signal files. Per-replicate aligments and sequences are available for download at <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/" TARGET=_BLANK>downloads page</A>. </P> <P> For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate <= 0.01 when comparing the number of peaks above said threshold to the number of peaks obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value ≤ 0.01 are considered to be significantly enriched compared to the input DNA control. </P> <h2>Release Notes</h2> <P> This is Release 2 (September 2011) of this track, which includes additional experiments. </P> <P> A few of the previously released Alignments have been replaced by updated versions. The affected database files include 'V2' in the name, and metadata is marked with "submittedDataVersion=V2", followed by the reason for replacement, "Resubmitted with correct alignment file". </P> <P> Previous versions of files are available for download from the <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/" TARGET=_BLANK>FTP site.</A> </P> <H2>Credits</H2> <P>These data were generated and analyzed by the labs of <A HREF="http://snyderlab.stanford.edu/" class="external text" title="http://snyderlab.stanford.edu/" target="_blank">Michael Snyder</a> at Stanford University and <A HREF="http://medicine.yale.edu/genetics/people/sherman_weissman.profile" class="external text" title="http://medicine.yale.edu/genetics/people/sherman_weissman.profile" target="_blank">Sherman Weissman</a> at Yale University. </P> <P> Contact: <A HREF="mailto:pcayting@stanf ord.edu" title="mailto:pcayting@stanf ord.edu" rel="nofollow" TARGET=_BLANK>Philip Cayting</A>. <!-- above address is (Philip Cayting) pcayting at stanford.edu --> </P> <H2>References</H2> <p> Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19706456" target="_blank"> Mapping accessible chromatin regions using Sono-Seq</a>. <em>Proc Natl Acad Sci U S A</em>. 2009 Sep 1;106(35):14926-31. </p> <p> Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/17568005" target="_blank"> Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies</a>. <em>Genome Res</em>. 2007 Jun;17(6):898-909. </p> <p> Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/14527995" target="_blank"> Distribution of NF-kappaB-binding sites across human chromosome 22</a>. <em>Proc Natl Acad Sci U S A</em>. 2003 Oct 14;100(21):12247-52. </p> <p> Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/17558387" target="_blank"> Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing</a>. <em>Nat Methods</em>. 2007 Aug;4(8):651-7. </p> <p> Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19122651" target="_blank"> PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls</a>. <em>Nat Biotechnol</em>. 2009 Jan;27(1):66-75. </p> <H2>Data Release Policy</H2> <P>Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the <EM>Restricted Until</EM> column on the track configuration page and the download page. The full data release policy for ENCODE is available <A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>