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diff --git a/general/datasets/HC_M2_1205_R/cases.rtf b/general/datasets/HC_M2_1205_R/cases.rtf deleted file mode 100644 index 3e78bb4..0000000 --- a/general/datasets/HC_M2_1205_R/cases.rtf +++ /dev/null @@ -1,60 +0,0 @@ -<p>This analysis has used 68 of BXD strains, the complete set of 13 CXB recombinant inbred strain sets, and a mouse diversity panel consisting of 16 inbred strains and a pair of reciprocal F1 hybrids (B6D2F1 and D2B6F1).</p>
-
-<p>The <a class="fs14" href="http://www.genenetwork.org/mouseCross.html#BXD" target="_empty">BXD</a> genetic reference population of recombinant inbred strains consists of approximately 80 strains. Approximately <a class="fs14" href="http://www.genenetwork.org/mouseCross.html#BXD" target="_empty">800</a> classical phenotypes from sets of 10 to 70 of these strains been integrated in the GeneNetwork. The BXD strains in this data set include 29 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs.</p>
-
-<p>The <a class="fs14" href="http://www.genenetwork.org/mouseCross.html#CXB" target="_empty">CXB</a> is the first and oldest set of recombinant inbred strains. Over <a class="fs14" href="http://www.genenetwork.org/mouseCross.html#CXB" target="_empty">500</a> classical phenotypes from these strains been integrated in the GeneNetwork. It is noteworthy that the CXB strains segregate for the hippocampal lamination defect (<em>Hld</em>),characterized by Nowakowski and colleagues (<a class="fs14" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=6536729&dopt=Citation" target="_empty">1984</a>). All of the CXBs have been recently genotyped at 13,377 SNPs.</p>
-
-<p><strong>Mouse Diversity Panel (MDP)</strong>. We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1. These strains were selected for several reasons:</p>
-
-<ul>
- <li>genetic and phenotypic diversity, including use by the <a class="fs14" href="http://aretha.jax.org/pub-cgi/phenome/mpdcgi?rtn=strains%2Flist&listmode=pri&typemode=all&genaltmode=no&submit1=%A0%A0Go%A0%A0" target="_empty">Phenome Project</a></li>
- <li>their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains</li>
- <li>their use by the <a class="fs14" href="http://www.complextrait.org" target="_empty">Complex Trait Consortium</a> to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA)</li>
- <li>genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)</li>
- <li>availability from The Jackson Laboratory</li>
-</ul>
-
-<p>All eight parents of the Collaborative Cross (129, A, C57BL/6J, CAST, NOD, NZO, PWK, and WSB) have been included in the MDP (noted below in the list). Twelve MDP strains have been sequenced, or are currently being resequenced by Perlegen for the NIEHS. This panel will be extremely helpful in systems genetic analysis of a wide variety of traits, and will be a powerful adjunct in fine mapping modulators using what is essentially an association analysis of sequence variants.</p>
-
-<ol>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/129.shtml" target="_empty">129S1/SvImJ </a><br />
- Collaborative Cross strain sequenced by NIEHS; background for many knockouts; Phenome Project A list</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/A.shtml" target="_empty">A/J</a><br />
- Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/AKR.shtml" target="_empty">AKR/J</a><br />
- Sequenced by NIEHS; Phenome Project B list</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/BALB.shtml" target="_empty">BALB/cByJ</a><br />
- STILL IN PROGRESS (samples did not pass quality control); Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project A list</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/BALB.shtml" target="_empty">BALB/cJ</a><br />
- Widely used strain with forebrain abnormalities (callosal defects); Phenome Project A list</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/C3H.shtml" target="_empty">C3H/HeJ</a><br />
- Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml" target="_empty">C57BL/6J</a><br />
- Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml" target="_empty">C57BL/6ByJ</a><br />
- Paternal substrain of B6 used to generate the CXB panel</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/CAST.shtml" target="_empty">CAST/Ei</a><br />
- Collaborative Cross strain sequenced by NIEHS; Phenome Project A list</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/DBA.shtml" target="_empty">DBA/2J</a><br />
- Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/KK.shtml" target="_empty">KK/HIJ</a><br />
- Sequenced by Perlegen/NIEHS</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/LG.shtml" target="_empty">LG/J</a><br />
- Paternal parent of the LGXSM panel</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/NOD.shtml" target="_empty">NOD/LtJ</a><br />
- Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/NZO.shtml" target="_empty">NZO/HILtJ</a><br />
- Collaborative Cross strain</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/PWD.shtml" target="_empty">PWD/PhJ</a><br />
- Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues</li>
- <li><a class="fs14" href="http://www.informatics.jax.org/external/festing/mouse/docs/PWK.shtml" target="_empty">PWK/PhJ</a><br />
- Collaborative Cross strain; Phenome Project D list</li>
- <li><a class="fs14" href=" " target="_empty">WSB/EiJ</a><br />
- Collaborative Cross strain sequenced by NIEHS; Phenome Project C list</li>
- <li>B6D2F1 and D2B6F1<br />
- F1 hybrids generated by crossing C57BL/6J with DBA/2J</li>
-</ol>
-
-<p>We have not combined data from reciprocal F1s because they have different Y chromosome and mitochondial haplotypes. Parent-of-origin effects (imprinting, maternal environment) may also lead to interesting differences in hippocampal transcript levels.</p>
-
-<p>These strains are available from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC.</p>
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