bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/ENCODE/downloadsMouse.html src/hg/htdocs/ENCODE/downloadsMouse.html index 1d1ffc3eb6a..2b5e6a3e4d8 100755 --- src/hg/htdocs/ENCODE/downloadsMouse.html +++ src/hg/htdocs/ENCODE/downloadsMouse.html @@ -15,143 +15,143 @@ <body> <!--#include virtual="/inc/encodeProject.topbar.html"--> <div class="encodeHeader"> <a href="/ENCODE/index.html"><img src="/images/gbLogoOnly.png" style="height:70%;" alt="ENCODE at UCSC" title="ENCODE at UCSC"></a> <span class="txt">Mouse ENCODE Downloads</span> <span class="encodeHeaderDates">2007 - 2012</span> </div> <div class="wrapper"> <div class="bar"><h4 class="title">Overview</h4></div> <div class="content"> <P>This page contains links to directories containing raw and processed data for mouse ENCODE data produced as part of the ENCODE production phase (September 2007 - December 2012). Formats are described on the UCSC Browser <A HREF="/FAQ/FAQformat.html" TARGET=_blank>File Format FAQ</A>. For bulk download, retrieval by - <A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/" TARGET=_blank>FTP</A> + <A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/" TARGET=_blank>FTP</A> is recommended along with rsync. Using rsync, for example "rsync -a -P - rsync://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeDir/wgEncodeFile ./", + rsync://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeDir/wgEncodeFile ./", has the advantage of starting up where it left off after a failure, when ran again.</P> </div><!--end content--> </div><!--end wrapper--> <div class="wrapper"> <div class="bar"><h4 class="title"><a - href="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/" + href="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/" title="Click to see files directory for mouse (mm9)">Mouse Genome Build NCBI37/mm9</A> <input type='button' class='buttonLink right' value='File search' onclick="window.location='../cgi-bin/hgFileSearch?db=mm9';" title='Search for downloadable files ...'></h4> </div> <div class="content"> <p> <TABLE class='itemTbl' BORDER=1 CELLSPACING=0> <TR> <td class='ltGray hd2' colspan=2>Bidirectional Promoters</td> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeNhgriBip/" TARGET=_BLANK>NHGRI BiP</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeNhgriBip/" TARGET=_BLANK>NHGRI BiP</A> </TD> <TD>NHGRI Elnitski Bidirectional Promoters</TD> </TR> <TR> <td class='ltGray hd2' colspan=2>Chromatin Accessibility</td> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/" TARGET=_BLANK>PSU DNaseI HS</A></TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/" TARGET=_BLANK>PSU DNaseI HS</A></TD> <TD>DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/" TARGET=_BLANK>UW DNaseI DGF</A></TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/" TARGET=_BLANK>UW DNaseI DGF</A></TD> <TD>DNaseI Digital Genomic Footprinting from ENCODE/University of Washington</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/" TARGET=_BLANK>UW DNaseI HS</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/" TARGET=_BLANK>UW DNaseI HS</A> </TD> <TD>DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington</TD> </TR> <TR> <td class='ltGray hd2' colspan=2>Histone Modification</td> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechHist/" TARGET=_BLANK>Caltech Histone</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechHist/" TARGET=_BLANK>Caltech Histone</A> </TD> <TD>Histone Modifications by ChIP-seq from ENCODE/Caltech</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/" TARGET=_BLANK>LICR Histone</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/" TARGET=_BLANK>LICR Histone</A> </TD> <TD>Histone Modifications by ChIP-seq from ENCODE/LICR</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/" TARGET=_BLANK>PSU Histone</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/" TARGET=_BLANK>PSU Histone</A> </TD> <TD>Histone Modifications by ChIP-seq from ENCODE/PSU</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/" TARGET=_BLANK>Stan/Yale Histone</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/" TARGET=_BLANK>Stan/Yale Histone</A> </TD> <TD>Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale</TD> </TR> <TR> <td class='ltGray hd2' colspan=2>Transcription Factor Binding Sites</td> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/" TARGET=_BLANK>Caltech TFBS</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/" TARGET=_BLANK>Caltech TFBS</A> </TD> <TD>Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/" TARGET=_BLANK>LICR TFBS</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/" TARGET=_BLANK>LICR TFBS</A> </TD> <TD>Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/" TARGET=_BLANK>PSU TFBS</A></TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/" TARGET=_BLANK>PSU TFBS</A></TD> <TD>Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/" TARGET=_BLANK>Stan/Yale TFBS</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/" TARGET=_BLANK>Stan/Yale TFBS</A> </TD> <TD>Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale</TD> </TR> <TR> <td class='ltGray hd2' colspan=2>RNA-seq</td> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechRnaSeq/" + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechRnaSeq/" TARGET=_BLANK>Caltech RNA-seq</A></TD> <TD>RNA-seq from ENCODE/Caltech</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/" TARGET=_BLANK>CSHL Long RNA-seq</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/" TARGET=_BLANK>CSHL Long RNA-seq</A> </TD> <TD>Long RNA-seq from ENCODE/CSHL</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/" TARGET=_BLANK>LICR RNA-seq</A> </TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/" TARGET=_BLANK>LICR RNA-seq</A> </TD> <TD>RNA-seq from ENCODE/LICR</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/" TARGET=_BLANK>PSU RNA-seq</A></TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/" TARGET=_BLANK>PSU RNA-seq</A></TD> <TD>RNA-seq from ENCODE/PSU</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/" TARGET=_BLANK>Stan/Yale RNA-seq</A></TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/" TARGET=_BLANK>Stan/Yale RNA-seq</A></TD> <TD>RNA-seq from ENCODE/Stanford</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/" TARGET=_BLANK>UW RNA-seq</A></TD> + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/" TARGET=_BLANK>UW RNA-seq</A></TD> <TD>RNA-seq from ENCODE/UW</TD> </TR> <TR> <td class='ltGray hd2' colspan=2>Other</td> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeFsuRepliChip/" + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeFsuRepliChip/" TARGET=_BLANK>FSU Repli-chip</A></TD> <TD>Replication Timing by Repli-chip from ENCODE/FSU</TD> </TR> <TR> - <TD><A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeMapability/" + <TD><A HREF="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeMapability/" TARGET=_BLANK>Mappability</A></TD> <TD>Mappability or Uniqueness of Reference Genome from ENCODE</TD> </TR> </TABLE> </p> </div><!--end content--> </div><!--end wrapper--> </BODY> </HTML>