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diff --git a/web/cross.html b/web/cross.html new file mode 100755 index 00000000..a30c11e5 --- /dev/null +++ b/web/cross.html @@ -0,0 +1,209 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>HTML Template</TITLE> +<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> +<LINK REL="stylesheet" TYPE="text/css" HREF='css/general.css'> +<LINK REL="stylesheet" TYPE="text/css" HREF='css/menu.css'> +<SCRIPT SRC="javascript/webqtl.js"></SCRIPT> +</HEAD> +<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> +<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> + <TBODY> + <TR> + <script language="JavaScript" src="/javascript/header.js"></script> + </TR> + <TR> + <TD bgColor=#eeeeee class="solidBorder"> + <Table width= "100%" cellSpacing=0 cellPadding=5><TR> + <!-- Body Start from Here --> + <TD vAlign=top width="100%" height=200 bgColor=#eeeeee> + +<P class="title">Mouse Cross Information <A HREF="/webqtl/main.py?FormID=editHtml"><img src="images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> + <A NAME="AKXD" class="subtitle"> +AKXD:</A> + +<Blockquote> +The AKXD recombinant inbred (RI) strains are derived from AKR/J (AK) and DBA/2J (D). All of these strains were made by Benjamin A. Taylor. </P> + +<P>All of the AKXD data in WebQTL is from an experiment by Kent Hunter and colleagues. WebQTL does not yet include a Phenotypes database for this strain set.</P> + +<P>How to obtain these strains: These strains are now cryopreserved. To rederive these strains please contact the Jackson Laboratory and see <a href="http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml" target="_blank" class="normal">http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml</a>. +</P> + +</Blockquote> + <A NAME="AXB" class="subtitle"></A><A NAME="BXA" class="subtitle"></A><A NAME="AXBXA" class="subtitle"> +AXB/BXA: +</A> +<Blockquote><P> +The AXB and BXA set of recombinant inbred (RI) strains were derived from a reciprocal cross between A/J (A) and C57BL/6J (B). Both parental strains have been sequenced, making this a particularly powerful set of RI strains for functional and genetic analyses. Data acquired using AXB and BXA subsets should be combined; the only difference being the polarity of intercross matings that generated (A x B)F1s and (B x A)F1s. AXB and BXA strains were all produced by Muriel Nesbitt at UCSD in the mid and late 1970s and first used in the early 1980s (Skamene et al., 1984; Peleg and Nesbitt, 1984; Marshal and Paigen, <a href="http://jaxmice.jax.org/library/notes/454a.htm" target="_blank" class="normal">1993</a>). The set was imported into The Jackson Laboratory by Beverly Paigen (Pgn) in the early 1990s. As of 2004, approximately 25 viable and fully independent AXB/BXA strains are available.</P> + +<P>Approximately 100 traits are currently included in the AXBXA Phenotypes database (Nov 2004). +</P> + +<P>Several nominally independent strains in the AXB and BXA sets are very closely related. These duplicates should not be used without special statistical precaution. The most obvious option is to combine and average data from these strains except when their phenotypes differ significantly (Taylor <a href="http://jaxmice.jax.org/library/notes/465b.html" target="_blank" class="normal">1996</a>; Williams et al., <a href="http://genomebiology.com/2001/2/11/research/0046" target="_blank" class="normal">2001</a>). + +<BR> +<BR>AXB13=AXB14: 92% identity +<BR>AXB18=AXB19=AXB20: 97 to 99% identity +<BR>BXA8=BXA17: 99.8% identity +</P> + +<P>How to obtain these strains: Please see <a href="http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml" target="_blank" class="normal">http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml</a>. +</P> + +</Blockquote> + <A NAME="BXD" class="subtitle"> +BXD: +</A> +<Blockquote><P> +The BXD set of recombinant inbred (RI) strains were derived by crossing C57BL/6J (B) and DBA/2J (D) and then inbreeding progeny for over 21 generations. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. A significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.</P> + +<P>BXD1 through BXD32 were produced by Benjamin A. Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Taylor, but from a second set of crosses initiated in the early 1990s. These strains are all available from the Jackson Laboratory, Bar Harbor, Maine. BXD43 through BXD99 were produced by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. <a href="http://www.biomedcentral.com/1471-2156/5/7" target="_blank" class="normal">2004</a>). These new strains have roughly twice the number of recombinations of conventional F2-derived RI straons. The new BXD strains are available now from Lu Lu and colleagues.</P> + +<P>The mitochondrial DNA of all BXD strains were typed by Jing Gu and Shuhua Qi (Nov 2004) using DNAs obtained from the Jackson Laboratory (BXD1 through 42) or from the UTHSC colony. This typing relied on a SNP marker identified by Jan Jiao in Weikuan Gu's laboratory at basepair position 9461 in the reference C57BL/6J mitochondrial sequence. Most strains have inherited mitochondria from C57BL/6J. However, the following strains have mitochondria with a DBA/2J allele at the UT-M-9461 SNP: BXD32, 61, 74, 76, 82, 89, 90, 91, 95, and BXD99. The only surprise in this list is that BXD32/TyJ has a DBA/2J mitochondrial genotype.</P> + +<P>Approximately 680 traits are currently included in the BXD Phenotypes database (Nov 2004).</P> + + +<P>How to obtain these strains: Please see <a href="http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml" target="_blank" class="normal">http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml</a>. +</P> + +</Blockquote> + + + <A NAME="BXH" class="subtitle"> +BXH:</A> +<Blockquote> +<P> +The BXH set were made by crossing female C57BL/6J (B) with male C3H/HeJ (H) mice. Benjamin Taylor created the initial 12 BXH recombinant inbred strains at The Jackson Laboratory in 1969. A second set of eight BXH strains were initiated by Linda Siracusa at the Kimmel Cancer Center in 1995. She selected for tyrosinase-negative albinos and her strains should not be used to map on Chr 7. Four of these new BXH strains are now also available from The Jackson Laboratory. The following are the old and new symbols for the four recent additions: + +<UL> +<LI>BXHA1/Sr = BXH20/Kcc +<LI>BXHA2/Sr = BXH21/Kcc +<LI>BXHB2/Sr = BXH22/Kcc +<LI>BXHE1/Sr = B6cC3-1/Kcc (backcrossed to B6 and a recombinant congenic) +</UL> + +<P>Approximately 135 traits are currently included in the BXH Phenotype database (Nov 2004).</P> + +<P>How to obtain these strains: Please see <a href="http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml" target="_blank" class="normal">http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml</a>. +</P> + +</Blockquote> + + + <A NAME="CXB" class="subtitle"> + +CXB:</A> +<Blockquote> +The CXB set is the first, oldest, and smallest group of mouse recombinant inbred strains. The materal strain is BALB/cBy and the paternal strain is C57BL/6By. They have been used extensively by immunologists and neurogeneticists. A total of 13 of these strains are now available. </P> + +<P>Over 450 traits are now included in the CXB Phenotype database (Nov 2004).</P> + + +<P>How to obtain these strains: Please see <a href="http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml" target="_blank" class="normal">http://jaxmice.jax.org/jaxmicedb/html/rcbinbred.shtml</a>. +</P> +</BLockquote> + + + <A NAME="LXS" class="subtitle">LXS:</A> + +<Blockquote><P> +The parental strains of the LXS recombinant inbred (RI) set are Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) strains. These parental strains have been phenotyped intensively by behavioral geneticists and neuropharmacologists for a decade. The LXS RI set has an intriguing history and trace back to an 8-way cross initiated in the 1950s by Gerald McClearn, the dean of mouse behavior genetics.</P> + +<P>The LXS panel has recently been genotyped at 330 microsatellite markers, and this panel can already be used to map Mendelian and quantitative trait loci.</P> + +<P>This is a new RI panel and only a small number of traits are currently included in the LXS Phenotype database (Nov 2004).</P> + + +<P>For information on the availability of the LXS strains please contact <a href="mailto:bennettb@colorado.edu" class="normal">Beth Bennett</span></a>. +</P> +</Blockquote> + + + <A NAME="B6D2F2" class="subtitle"> +B6D2F2:</A> + <Blockquote> + +<P> +Fifty-six <i>Filial generation 2</I> (F2) mice were generated by crossing C57BL/6J (B6) and DBA/2J (D2) stock from the Jackson Laboratory. The F1s were mated reciprocally to create B6D2F2 and D2B6F2 progeny. At present , WebQTL includes one large microarray data set (Affymetrix M430) for the entire brain of these F2 progeny.</P> + +<P> +For further information, please contact <A HREF="mailto:belknajo@ohsu.edu" class="normal">John Belknap</A>, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland VA Medical Center, Portland, OR 97239.</P> +</Blockquote> + + + + <A NAME="B6BTBRF2" class="subtitle"> +B6BTBRF2:</A> + +<Blockquote> +This cross consists of a subset of 60 F2 progeny generated by crossing C57BL/6J and BTBR strains. All of these cases are homozygous for the spontaneous obese mutation in the leptin gene (Lep-ob/ob). Metabolic function, liver mRNA expression (Agilent platform), and other physiological and molecular traits related to type 2 diabetes and obesity were quantified. Liver gene expression data were generated by Hong Lan and Alan Attie at The University of Wisconsin-Madison. Please contact Drs.<A HREF="mailto:attie@biochem.wisc.edu" class="normal"> Alan Attie</A> regarding use of this data set in publications or projects. +</Blockquote> + + <A NAME="MDP" class="subtitle"> + +MDP:</A> +<Blockquote> +The Mouse Diversity Panel is simply a composite of common and wild inbred strains and even some isogenic F1 hybrids. </P> + +<P>Over 1000 traits were downloaded from the <A href="http://phenome.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/home">Mouse Phenome Database</A> at The Jackson Laboratory in June 2006 and implemented in GeneNetwork July 2006.</P> + +<P>When using the MPD please cite this URL: +<A HRED="http://www.jax.org/phenome">http://www.jax.org/phenome</A>. This is the MPD's best known location and is usually preferable to the longer dynamic system URLs that may appear in URL address fields. + + +<P>Publications: + +<P>Grubb SC, Churchill GA, Bogue MA (2004) A collaborative database of inbred mouse strain characteristics. Bioinformatics. 20:2857-9. PMID: 15130929 + +<P>Bogue MA, Grubb SC (2004) The mouse phenome project. Genetica 122:71-74. PMID: 15619963 + +<P>To cite specific phenotyping data in the MPD, a format similar to this may be used. (Please be sure you have read and agree with our user agreement for taking and using MPD data.) + +<P>Investigators. Project Title. MPD accession#. Mouse Phenome Database Web Site, The Jackson Laboratory, Bar Harbor, Maine USA. World Wide Web (URL: http://www.jax.org/phenome, month and year of download ). + +<P>Example: +<P>Wahlsten D, Crabbe JC. Comparative study of activity, anxiety, motor learning, and spatial learning in two laboratories. MPD:108. Mouse Phenome Database Web Site, The Jackson Laboratory, Bar Harbor, ME USA. World Wide Web (URL: http://www.jax.org/phenome, July 2004). + +<P>Each phenotyping project in the MPD is assigned an accession number having the format MPD:NNN, where NNN is an integer. Accession numbers are displayed in the projects index and the individual project detail pages. + + +<P>How to obtain these strains: Please see <a href="http://jaxmice.jax.org/jaxmicedb/html/inbred.shtml" target="_blank" class="normal">http://jaxmice.jax.org/jaxmicedb/html/inbred.shtml</a>. +</P> +</BLockquote> + +<P class="subtitle"> About this file:</P> +<Blockquote><P> The file started, Nov 5, 2004 by RWW. Last update by RWW, Nov 6, 2004. EJC June 6, 2005. RWW, July 13, 2006</P></Blockquote> + </TD> + + <!-- Body End Here --> + </TR></TABLE> + </TD> + </TR> + <TR> + <TD align=center bgColor=#ddddff class="solidBorder"> + <!--Start of footer--> + <TABLE width="90%"> + <script language='JavaScript' src='/javascript/footer.js'></script> + </TABLE> + <!--End of footer--> + </TD> + </TR> +</TABLE> +<!-- /Footer --> +<script language="JavaScript" src="javascript/menu_new.js"></script> +<script language="JavaScript" src="javascript/menu_items.js"></script> +<script language="JavaScript" src="javascript/menu_tpl.js"></script> +<script language="JavaScript"> + <!--// + new menu (MENU_ITEMS, MENU_POS); + //--> +</script> +<script src="http://www.google-analytics.com/urchin.js" type="text/javascript"> +</script> +<script type="text/javascript"> +_uacct = "UA-3782271-1"; +urchinTracker(); +</script> +</BODY> +</HTML> |