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/wgEncodeLicrHistone.html src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html index 1b52ccc55c8..977df3a2434 100644 --- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html +++ src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html @@ -1,164 +1,164 @@ <H2>Description</H2> <P> This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq (Robertson <EM> et al.</EM>, 2007) to identify transcription factor binding sites and chromatin modification profiles in many mouse (C57Bl/6) tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells. </P> <P> In specific, the Ren lab examined RNA polymerase II (PolII), co-activator protein p300, the insulator protein CTCF, and two chromatin modification marks H3K4me3 and H3K4me1 due to their demonstrated utilities in identifying promoters, enhancers and insulator elements (Barski <EM>et al.</EM>, 2007; Blow <EM>et al.</EM>, 2010; Heintzman <EM>et al.</EM>, 2009; Kim <EM>et al.</EM>, 2007; Kim <EM> et al.</EM>, 2005a; Visel <EM>et al.</EM>, 2009). Enrichment of H3K4me3 or PolII signals is a strong indicator of active promoter, while the presence of p300 or H3K4me1 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. For each transcription factor or chromatin mark in each tissue, ChIP-seq was carried out with at least two biological replicates. Each experiment produced 20-30 million monoclonal, uniquely mapped tags. </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, 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). </DD> <DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on processed data.</DD> </DL> </P> <H2>Methods</H2> <P> Cells were grown according to the approved <A HREF="/ENCODE/protocols/cell/mouse" TARGET=_BLANK>ENCODE cell culture protocols</A>. </P> <P><DT><B><I>Enrichment and Library Preparation</I></B></DT> Chromatin immunoprecipitation was performed according to <A HREF="http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" TARGET=_BLANK>Ren Lab ChIP Protocol</A>. </P> <P> Library construction was performed according to <A HREF="http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf" TARGET=_BLANK>Ren Lab Library Protocol</A>. </P> <P><DT><B><I>Sequencing and Analysis</I></B></DT> Samples were sequenced on Illumina Genome Analyzer II Genome Analyzer IIx, and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (Langmead <EM>et al.</EM>, 2009) with a seed length of 25 and allowing up to two mismatches. Only the sequences that mapped to one location were used for further analysis. Of those sequences, clonal reads, defined as having the same start position on the same strand, were discarded. BED and wig files were created using custom perl scripts. </P> <H2>Credits</H2> <P> These data were generated and analyzed in <A HREF="http://licr-renlab.ucsd.edu/" TARGET=_BLANK>Bing Ren's laboratory</A> at the Ludwig Institute for Cancer Research. </P> <P> Contact: <A HREF="mailto:y7shen@ucsd. edu">Yin Shen</A> <!-- above address is y7shen at ucsd.edu --> </P> <H2>References</H2> <p> Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. <a href="https://www.ncbi.nlm.nih.gov/pubmed/17512414" target="_blank"> High-resolution profiling of histone methylations in the human genome</a>. <em>Cell</em>. 2007 May 18;129(4):823-37. </p> <p> Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/20729851" target="_blank"> ChIP-Seq identification of weakly conserved heart enhancers</a>. <em>Nat Genet</em>. 2010 Sep;42(9):806-10. </p> <p> Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19295514" target="_blank"> Histone modifications at human enhancers reflect global cell-type-specific gene expression</a>. <em>Nature</em>. 2009 May 7;459(7243):108-12. </p> <p> Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. <a href="https://www.ncbi.nlm.nih.gov/pubmed/17382889" target="_blank"> Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome</a>. <em>Cell</em>. 2007 Mar 23;128(6):1231-45. </p> <p> Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/15899964" target="_blank"> Direct isolation and identification of promoters in the human genome</a>. <em>Genome Res</em>. 2005 Jun;15(6):830-9. </p> <p> Langmead B, Trapnell C, Pop M, Salzberg SL. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank"> Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>. <em>Genome Biol</em>. 2009;10(3):R25. </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> Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19212405" target="_blank"> ChIP-seq accurately predicts tissue-specific activity of enhancers</a>. <em>Nature</em>. 2009 Feb 12;457(7231):854-8. </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>