b663a1b6e346124ef34608ca7062c285aa6a7587 lrnassar Tue Dec 3 10:21:31 2019 -0800 Added italics in response to CR refs #24579 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 35bf828..c53b675 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -122,31 +122,31 @@ href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack&hicAndMicroC=full" target="_blank">hg38</a> as well as the <a href=#081018>Interact format used in GeneHancer</a> for low-density interactions.</p> <p> Information and examples of displaying your own Hi-C data can be found on the <a href="help/hic.html">hic track format help page</a>. <a name="110519"></a> <h2>Nov. 5, 2019 Expanded CRISPR track released for mouse (GRCm38/mm10)</h2> <p> We are pleased to announce the release of an expanded <a href="../cgi-bin/hgTracks?db=mm10&hideTracks=1&knownGene=pack&crisprAllTargets=pack&position=chr1:11186551-11186838" target="_blank">CRISPR Targets track</a> for the mouse (GRCm38/mm10) assembly. This track shows the DNA sequences targetable by CRISPR RNA guides -using the Cas9 enzyme from S. pyogenes (PAM: NGG) over the entire mouse genome. CRISPR target +using the Cas9 enzyme from <i>S. pyogenes</i> (PAM: NGG) over the entire mouse genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool <a href="http://crispor.tefor.net/" target="_blank">CRISPOR</a>. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. </p> <p class="text-center"> <img class='text-center' src="../images/mm10CrisprAll.png" width='800' alt="CrisprAllTargets track"> </p> <p> We would like to thank Maximilian Haeussler, Hiram Clawson, and Lou Nassar for their effort creating and releasing this data track.</p> <a name="110119"></a> <h2>Nov. 1, 2019 New ENCODE 3 Regulation super-track set available on mouse (GRCm38/mm10) assembly</h2> @@ -337,31 +337,31 @@ setting on the right quickly draws attention to the track with the highest signal within the composite group.</p> <p> The new setting can be found for signal tracks within a composite group under the "Data view scaling:" options. <p class="text-center"> <img class='text-center' src="../images/groupAutoSetting.png" width='400' alt="Scaling options"> </p> <a name="100919"></a> <h2>Oct. 9, 2019 Expanded CRISPR track released for human (hg38/GRCh38)</h2> <p> We are pleased to announce the release of an expanded <a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack&crisprAllTargets=pack&position=chr7:116397500-116398000" target="_blank">CRISPR Targets track</a> for the human hg38/GRCh38 assembly. This track shows the DNA sequences targetable by CRISPR RNA guides -using the Cas9 enzyme from S. pyogenes (PAM: NGG) over the entire human genome. CRISPR target +using the Cas9 enzyme from <i>S. pyogenes</i> (PAM: NGG) over the entire human genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool <a href="http://crispor.tefor.net/" target="_blank">CRISPOR</a>. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. </p> <p class="text-center"> <img class='text-center' src="../images/crisperAllTargetsHg38.png" width='800' alt="CrisprAllTargets track"> </p> <p> We would like to thank Maximilian Haeussler, Hiram Clawson, and Conner Powell for their effort creating and releasing this data track.</p> <a name="09172019"></a> <h2>Sep. 17, 2019 New GRC Incident track for Chicken (galGal6) and Zebrafish (danRer11) @@ -583,31 +583,31 @@ <p> You can read more about how these tracks were created on the <a href="../../cgi-bin/hgTrackUi?db=hg38&g=transMapV5" target="_blank">track description page</a> for the hg38/GRCh38 version of these tracks. The TransMapV4 data can still be found in our <a href="http://hgdownload.soe.ucsc.edu/gbdb/" target="_blank">download server</a>.</p> <p> Thanks to Mark Diekhans and Lou Nassar for their work in creating and releasing these tracks.</p> <a name="070919"></a> <h2>Jul. 9, 2019 Expanded CRISPR track released for human (hg19/GRCh37)</h2> <p> We are pleased to announce the release of an expanded <a href="../cgi-bin/hgTracks?db=hg19&hideTracks=1&knownGene=pack&crisprAllTargets=pack&position=chr7:116397500-116398000" target="_blank">CRISPR Targets track</a> for the human hg19/GRCh37 assembly. This track shows the DNA sequences targetable by CRISPR RNA guides -using the Cas9 enzyme from S. pyogenes (PAM: NGG) over the entire human genome. CRISPR target +using the Cas9 enzyme from <i>S. pyogenes</i> (PAM: NGG) over the entire human genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool <a href="http://crispor.tefor.net/" target="_blank">CRISPOR</a>. </p> <p class="text-center"> <img class='text-center' src="../images/crisprAll.png" width='850' alt="CrisprAllTargets track"> </p> <p> We would like to thank Maximilian Haeussler, Hiram Clawson, and Daniel Schmelter for their effort creating, developing, and releasing this data track.</p> <a name="070119"></a> <h2>Jul. 1, 2019 New DGV Gold Standard track for human (hg19/GRCh37)</h2> <p> We are pleased to announce the DGV Gold Standard track for human (hg19/GRCh37). This track displays @@ -2835,31 +2835,31 @@ By default, only the <i>Common SNPs (150)</i> are visible in the browser; other tracks must be made visible using the track controls. <i>All SNPs (150)</i> tracks reside in the "Variation" group category for the hg19 and hg38 browsers.</p> <p> These tracks were produced at UCSC by Angie Hinrichs and checked for quality by Cath Tyner. We'd like to thank the dbSNP group at NCBI for providing access to these data.</p> <a name="081717"></a> <h2>Aug. 17, 2017 New CRISPR track for Chinese hamster</h2> <p> A new <a href="../cgi-bin/hgTrackUi?db=criGri1&g=crispr" target="_blank">CRISPR/Cas9</a> track is now available for the Chinese hamster (C_griseus_v1.0/<a href="../cgi-bin/hgGateway?db=criGri1" target="_blank">criGri1</a>) assembly.</p> <p> This track shows regions of the genome within 200 bp of transcribed regions and DNA sequences -targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG). CRISPR target +targetable by CRISPR RNA guides using the Cas9 enzyme from <i>S. pyogenes</i> (PAM: NGG). CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms using the <a href="http://crispor.tefor.net/" target="_blank">CRISPOR</a> tool.</p> <p> The details page for each target contains a wealth of information related to the target, such as the <a href="http://dx.doi.org/10.1038/nbt.2647" target="_blank">MIT Specificity score</a>, <a href="http://dx.doi.org/10.1038/nmeth.3543" target="_blank">Moreno-Mateos Efficiency Score</a>, <a href="http://dx.doi.org/10.1038/nbt.3437" target="_blank">Doench/Fusi Efficiency Score</a>, and any off-targets.</p> <p> If you would like us to generate this track for another assembly, please notify us at <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>.</p> <!-- above address is genome at soe.ucsc.edu --> @@ -3424,31 +3424,31 @@ target="_blank">video tutorial</a>, shows how to use the Genome Browser's multi-region viewing mode to substitute these sequences, along with their annotations, into the main chromosomes of this assembly, as well as other genome assemblies with alternate haplotypes. The video was produced by Robert Kuhn and David Gibson.</p> <p> See our <a href="../training/vids">video page</a> for a full list of our video offerings.</p> <a name="110716"></a> <h2>Nov. 7, 2016 New CRISPR track for many assemblies</h2> <p> A new CRISPR/Cas9 track has been released for the human (hg38, hg19), mouse (mm10), rat (rn5), zebrafish (danRer7), C. elegans (ce10), D. melanogaster (dm6), yeast (sacCer3) and C. intestinalis (ci2) assemblies.</p> <p> This track shows regions of the genome within 200bp of transcribed regions and DNA sequences -targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG). CRISPR target +targetable by CRISPR RNA guides using the Cas9 enzyme from <i>S. pyogenes</i> (PAM: NGG). CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms using the tool <a href="http://crispor.org">crispor.org</a>.</p> <p> The details page for each target contains a wealth of information related to the target, such as the <a href="http://dx.doi.org/10.1038/nbt.2647" target="_blank">MIT Specificity score</a>, <a href="http://www.nature.com/nmeth/journal/v12/n10/full/nmeth.3543.html" target="_blank">Moreno-Mateos Efficiency Score</a>, <a href="http://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design" target="_blank">Doench/Fusi Efficiency Score</a>, and any off-targets.</p> <p> If you would like us to generate this track for another assembly, please notify us at <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>.</p> <!-- above address is genome at soe.ucsc.edu -->