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diff --git a/general/datasets/Eye_M2_0908_R_NB/cases.rtf b/general/datasets/Eye_M2_0908_R_NB/cases.rtf deleted file mode 100644 index 552d4a5..0000000 --- a/general/datasets/Eye_M2_0908_R_NB/cases.rtf +++ /dev/null @@ -1,57 +0,0 @@ -<p>This is the complete and final HEIMED data set. HEIMED consists of expression data for 103 genetically defined lines of mice with standard errors of the mean. Almost all animals are young adults between 50 and 80 days of age (Table 1, maximum age is 123 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, reciprocal F1s between C57BL/6J and DBA/2J, and several mutant and knockout lines. We have combined all common strains, F1 hybrids, and mutants into a group called the Mouse Diversity Panel (MDP). Four lines, namely, C57BL/6J (B6), DBA/2J (D2), and the pair of B6D2F1 and D2B6F1 hybrids are common to both the MDP and the BXD set. This is a breakdown of cases that are part of HEIMED:</p>
-
-<ol>
- <li>68 BXD strains. The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. Only one of these strains, BXD24 (know also known as BXD24b), has retinal degeneration (a spontaneous mutation). The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. <a class="normalsize" href="http://www.biomedcentral.com/1471-2156/5/7" target="_blank">2004</a>). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from <a class="normalsize" href="mailto:lulu@nb.utmem.EDU" target="_blank">Lu Lu</a> and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA.</li>
- <li>35 MDP lines, including 26 inbred strains representing closely related substrains (e.g, BALB/cJ and BALB/cByJ), many of the most widely used common <em>Mus musculus domesticus</em> inbred strains (e.g., C57BL/6J and 129S1/SvImJ), inbred but wild-derived representatives of common subspecies (<em>Mus musculus domesticus</em>, e.g, WSB/EiJ; <em>M. musculus musculus</em>, e.g., CZECHII/EiJ; <em>M. musculus molossinus</em>, e.g., MOLF/EiJ; <em>M. musculus castaneus</em>, e.g., CAST/EiJ); and even one different species of mouse (<em>Mus spicilegus</em>, PANCEVO/EiJ). The MDP also includes the reciprocal F1 hybrids (B6D2F1 and D2B6F1) and the following 6 KO lines and the <em>Nyx-nob</em> mutant:</li>
- <li>6 knockouts (KO), including a KO of <em>Rpe65</em>, and 5 <a class="normalsize" href="http://www.deltagen.com/" target="_empty">DeltaGen Inc.</a> knockout lines provided by Dr. Ted Choi. These KO lines have had a bacterial lacZ construct inserted into the gene. The endogenous promoter drives expression of beta-galactosidase. RT-PCR analysis detects a gene transcript in most tissues. The following KOs from DeltaGen were studied: <em>Gabra1, <a class="normalsize" href="http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&key=40055" target="_blank">Gabbr1</a>, Gnb1, <a class="normalsize" href="http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&key=40062" target="_blank">Gpr19</a>,</em> and <em>Clcn3</em>. We also included one spontaneous mutant of the <a class="normalsize" href="http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&key=6514" target="_blank">nyctalopin</a> (<em>Nyx</em> no b wave "nob") gene (Pardue et al., <a class="normalsize" href="http://www.iovs.org/cgi/reprint/39/12/2443" target="_blank">1998</a>) that is on a BALB/cByJ background.</li>
-</ol>
-
-<p><strong>Rod photoreceptor degeneration in inbred mice</strong>: Six strains of mice included in HEIMED suffer from severe loss of photoreceptors (mainly rods) and have the equivalent of night blindness in human patients. The death of photoreceptors in these strains occurs by one to two months of age and is often caused by the <em>retinal degeneration 1 (rd1)</em> mutant allele in the rod cyclic-GMP phosphodiesterase 6 beta subunit gene (<em>Pde6b</em>). The following strains are known to have photoreceptor degeneration: C3H/HeJ, FVB/NJ, MOLF/EiJ, SJL/J and BXD24/TyJ. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEIMED data set.</p>
-
-<p>As expected (Dickerson LW et al., <a class="normalsize" href="http://www.ncbi.nlm.nih.gov/sites/entrez/12470859" target="_blank">2002</a>) and as judged from the absence of rhodopsin expression, one of the DeltaGen KO lines (chloride ion channel 3, <em>Clcn3</em>) also has retinal degeneration: B6129P2F2N1-Clcn3. Degeneration in this strain is likely to include all rods and all cones. The cone defect is obvious from the decrease in expression of <em>Gnat2</em>, a gene associated with cones and achromatopsia in mice and humans.</p>
-
-<p>Lines of mice were selected using the following criteria:</p>
-
-<ul>
- <li>genetic and phenotypic diversity, including use by the <a class="normalsize" href="http://aretha.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/introducing" target="_empty">Phenome Project</a></li>
- <li>representation of a fairly wide variety of different subspecies of Mus</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="normalsize" href="http://www.complextrait.org" target="_empty">Complex Trait Consortium</a> to make the Collaborative Cross (Tel Aviv/Wellcome, Oak Ridge/DOE, and Perth/UWA)</li>
- <li>genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS)</li>
- <li>interesting mutations or knockouts affecting genes with high expression in the eye</li>
- <li>general availability from The Jackson Laboratory. The only exception are the DeltaGen KO mice.</li>
-</ul>
-
-<p>We have included all eight parents of the Collaborative Cross (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/LtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ) in the MDP. Fourteen MDP strains have been partially sequenced by Perlegen for the NIEHS, including including 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, C3H/HeJ, CAST/EiJ, DBA/2J, FVB/NJ, KK/HlJ, MOLF/EiJ, NOD/LtJ, NZW/LacJ, PWD/PhJ, and WSB/EiJ (see the GeneNetwork SNP Browser for data, details, and see <a class="normalsize" href="http://mouse.perlegen.com/mouse/download.html" target="_empty">Perlegen's excellent data resources and browser</a>).</p>
-
-<ol>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/129.shtml" target="_empty">129S1/SvImJ </a>: Collaborative Cross strain sequenced by NIEHS; background for many knockouts (R1 ES cell line); Phenome Project A list. This strain (JAX No 002448, aka 129S1/Sv-++Kitl/+) carries hypopigmentation mutations (white bellied chinchilla) of the tyrosinase gene on Chr 7 and a mutant allele of the steel (Kitl) gene. It is also a <em>cone photoreceptor function loss 3</em> mutant (<em>Cpfl3</em> allele) of the <em>Gnat2</em> gene that is a model for achromatopsia (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/002448.html" target="_empty">002448</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/A.shtml" target="_empty">A/J</a>: Collaborative Cross strain sequenced by Perlegen/NIEHS; parent of the AXB/BXA panel. A tyrosinase (<em>Tyr c</em> allele) albino mutant. This strain is particularly sensitive to light-induced photoreceptor loss (Danciger et al., 2007). (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000646.html" target="_empty">000646</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/BALB.shtml" target="_empty">BALB/cByJ</a>: Sequenced by NIEHS; maternal parent of the CXB panel; Phenome Project old group A list. A tyrosinase (<em>Tyr c</em> allele) albino mutant and also a tyrosinase related protein 1 (<em>Tyrp1 b</em>) brown allele mutant. Small brain, not aggressive (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/001026.html" target="_empty">001026</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/BALB.shtml" target="_empty">BALB/cJ</a>: Phenome Project A list. A tyrosinase (<em>Tyr c</em> allele) albino mutant and also a tyrosinase related protein 1 (<em>Tyrp1 b</em>) brown allele mutant. Large brain and aggressive (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000651.html" target="_empty">000651</a>)</li>
- <li><a class="normalsize" href="hhttp://phenome.jax.org/pub-cgi/phenome/mpdcgi?rtn=strains/details&aname=BXSB/MpJ" target="_empty">BXSB/MpJ</a>: A white-bellied agouti strains with interesting autoimmune disease restricted to males that is associated with a mutation in the <em>Yaa</em> gene that causes glomerulonephritis, a dramatic increase in number of peripheral monocytes, and pre-B-cell deficiency (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000740.html" target="_empty">000740</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/C3H.shtml" target="_empty">C3H/HeJ</a>: The Heston (He) substrain with a wildtype agouti (A allele) coat color. Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project old group A list. Important to note for this eye expression dataset, C3H/HeJ is a <em>Pdeb6 rd1</em> mutant with near total photoreceptor loss at as early as postnatal day 30. Also a <em>Tlr4</em> mutant that is endotoxin resistant. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000659.html" target="_empty">000659</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml" target="_empty">C57BL/6J</a>: Sequenced by NIH/NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list. Single most widely used inbred strain of mouse. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000664.html" target="_empty">000664</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml" target="_empty">C57BLKS/J</a>: Black Kaliss strain (non-agouti a allele) derived from C57BL/6J, but genetically contaminated at some point mainly with DBA/2J and then reinbred. Now at the Jackson Laboratory. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000662.html" target="_empty">000662</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/CAST.shtml" target="_empty">CAST/EiJ</a>: A wild-derived inbred <em>Mus musculus castaneus</em> strain. Samples of this subspecies were captured in Southeast Asia. One of three wild-derived strains in the Collaborative Cross sequenced by NIEHS; Phenome Project A list. CAST/Ei and CAST/EiJ are the same strain. The addition of the "J" is trivial and was added when stock were transferred from Dr. Eicher's lab to the Jackson Laboratory production facility in about 2004. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000928.html" target="_empty">000928</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/CBA.shtml" target="_empty">CBA/CaJ</a>: Agouti strain from the Jackson Laboratory. Wildtype pigment genes. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000654.html" target="_empty">000654</a>)</li>
- <li><a class="normalsize" href="http://jaxmice.jax.org/strain/001144.html" target="_empty">CZECHII/EiJ</a>: Czech 2 is a wild-derived inbred strain <em>M. musculus musculus</em> strain. Samples of this subspecies were caught in the Czech Republic and inbred at the Jackson Laboratory by Eva Eicher. White-bellied agouti. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/001144.html" target="_empty">001144</a>).</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/DBA.shtml" target="_empty">DBA/2J</a>: The dilute, brown, agouti (dba) strain is the oldest inbred strain of mouse. Inbreeding was started in 1909 by Little. A tyrosinase related protein 1 (<em>Tyrp1 b</em>) brown allele mutant. A myosin 5a (<em>Myo5a d</em>) dilute allele mutant. Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project old A group list. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000671.html" target="_empty">000671</a>)</li>
- <li><a class="normalsize" href="http://jaxmice.jax.org/strain/001800_2.html" target="_empty">FVB/NJ</a>: Friend's leukemia virus B (FVB) strain. Sequenced by Perlegen/NIEHS and Celera. <em>Tyr</em> c locus albino and a <em>Pdeb6 rd1</em> mutant derived from Swiss mice at NIH. This has been the most common strain used to make transgenic mice due to large and easily injected oocytes; Phenome Project A list (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/001800.html" target="_empty">001800</a>).</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/KK.shtml" target="_empty">KK/HlJ</a>: K Kondo's (KK) Kasukabe strain is a homozygous age-related hearing loss (<em>ahl</em>) allele mutant of the <em>Cdh23</em> gene. A <em>Tyr</em> c locus albino strain. Males have a form of type 2 diabetes. Sequenced by Perlegen/NIEHS. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/002106.html" target="_empty">002106</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/LG.shtml" target="_empty">LG/J</a>: Large (LG) strain. Paternal parent of the Large-by-Small set of RI strains made by James Cheverud and colleagues (the LGXSM panel, not to be confused with the LongXShort or LXS panel). A <em>Tyr</em> c locus albino strain. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000675.html" target="_empty">000675</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/LP.shtml" target="_empty">LP/J</a>: White-bellied agouit strain with a piebald mutation in the endothelin receptor type B <em>Ednrb</em> gene from at the Jackson Laboratory. Some reduction in melanocytes in choroid of eye due to neural creast migration abnormalities. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000676.html" target="_empty">000676</a>)</li>
- <li><a class="normalsize" href="http://jaxmice.jax.org/strain/000550_2.html" target="_empty">MOLF/EiJ</a>: A wild-derived inbred strain derived from <em>M. musculus molossinus</em> samples camputered in Fukuoka, Japan. This strain has the retinal degeneration <em>rd1</em> allele in <em>Pde6b</em>. There appears to have been some genetic contamination of this strain with conventional inbred strains in the past several decades (F. Pardo, personal communication to RWW, August 2006). However, the strain is currently fully inbred. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000550.html" target="_empty">000550</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/NOD.shtml" target="_empty">NOD/LtJ</a>: Non-obese diabetic strain, originally from M. Hattori in Kyoto, Japan. This is the Edward Leiter (Lt) substrain from the Jackson Laboratory. Collaborative Cross strain sequenced by NIEHS; Phenome Project B list. Homozygous age-related hearing loss (<em>ahl</em>) allele mutant of the <em>Cdh23</em> gene. A <em>Tyr</em> c locus albino strain. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/001976.html" target="_empty">001976</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/NZO.shtml" target="_empty">NZO/HlLtJ</a>: New Zealand Obese strain. This is a severely obese and hypertensive strain. Males often develop a type 2 diabetes. Collaborative Cross strain. Agouti coat color. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/002105.html" target="_empty">002105</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/NZB.shtml" target="_empty">NZB/BlNJ</a>: New Zealand Black inbred strain from Bielschowsky (BL, substrain is "B lowercase L N", not "BiN") now maintained at the Jackson Laboratory. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000684.html" target="_empty">000648</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/NZW.shtml" target="_empty">NZW/LacJ</a>: New Zealand White strain from the Laboratory Animal Center (Carshalton, UK), now maintained at the Jackson Laboratory. Carries the <em>Tyr</em> c locus albino mutation, the pink-eye dilution mutation in the <em>Oca2</em> or p locus, and the brown allele at <em>Tyrp1</em>. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/001058.html" target="_empty">001058</a>)</li>
- <li><a class="normalsize" href="http://jaxmice.jax.org/strain/001384.html" target="_empty">PANCEVO/EiJ</a>: PANCEVO/EiJ is a wild-derived inbred strain from the <em>Mus spicilegus</em> samples caught in the Pancevo, Serbia. This species of mouse is also known as the Steppe mouse (taxon identifier <a class="normalsize" href="http://www.uniprot.org/taxonomy/10103" target="_empty">10103</a>). <em>M. spicilegus</em> is a colonial <a class="normalsize" href="http://www3.interscience.wiley.com/journal/119160997/abstract?CRETRY=1&SRETRY=0" target="_empty">mound-building species</a>. No known ocular or retina mutations, but the expression level of <em>Gnat2</em> is low in this strain, either due to a 3' UTR length variant or possible achromatosia (cone degeneration) (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/001384.html" target="_empty">001384</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/PWD.shtml" target="_empty">PWD/PhJ</a>: A wild-derived <em>Mus musculus musculus</em> agouti strain inbred from samples caught near Prague, Czech Republic. Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/004660.html" target="_empty">004660</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/PWK.shtml" target="_empty">PWK/PhJ</a>: A wild-derived <em>Mus musculus musculus</em> inbred strain from samples caught near Lhotka, Czech Republic. Collaborative Cross strain; Phenome Project D list. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/003715.html" target="_empty">003715</a>)</li>
- <li><a class="normalsize" href="http://www.informatics.jax.org/external/festing/mouse/docs/SJL.shtml" target="_empty">SJL/J</a>: Swiss Webster inbred strain from Jim Lambert's lab at the Jackson Laboratory. This strain has the retinal degeneration <em>rd1</em> allele in <em>Pde6b</em>. It also carries both the <em>Tyr</em> c albino mutation and the pink-eye dilution mutation in the <em>Oca2</em> or p locus. Highly aggressive males. (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/000686.html" target="_empty">000686</a>)</li>
- <li><a class="normalsize" href="http://jaxmice.jax.org/strain/001145.html" target="_empty">WSB/EiJ</a>: Watkin Star line B (or "wild son-of-a-bitch") is a wild-derived <em>Mus musculus domesticus</em> inbred strain from samples caught in Maryland, USA. A Collaborative Cross strain sequenced by NIEHS; Phenome Project C list (JAX Stock Number: <a class="normalsize" href="http://jaxmice.jax.org/strain/001145.html" target="_empty">001145</a>)</li>
- <li>B6D2F1 and D2B6F1 (also listed as BDF1 and DBF1 in some graphs and tables): F1 hybrids generated by crossing C57BL/6J with DBA/2J. These black reciprocal F1 can be used to detect dominance effects. Comparison of the two reciprocal F1s can be used to detect parental origin (imprinting) effects. The D2B6F1 animals are currently available from the Jackson Laboratory as a special order.) (JAX Stock Number for B6D2F1 hybrids obtained from the Jackson Laboratory, aka B6D2F1/J <a class="normalsize" href="http://jaxmice.jax.org/strain/100006.html" target="_empty">100006</a>)</li>
-</ol>
-
-<p>Most of the common inbred strains harbor mutations in genes the control pigmentation (Silvers, <a class="normalsize" href="http://www.informatics.jax.org/wksilvers/index.shtml" target="_empty">2008</a> and material above in this INFO file). These gene include the albino and chinchilla alleles of the tyrosinase gene (<em>Tyr</em>, or human <em>OCA1</em>), the brown allele of the tyrosinase related protein 1 (<em>Tyrp1</em>), the pink-eye dilution allele of <em>Oca2</em> (probe set 1418211), the non-agouti (black) and white-bellied alleles of the agouti signaling protein <em>Asip</em>, the steel allele of <em>Kitlg</em>, the dilute allele of <em>Myo5a</em> (probe set 1419754), and the piebald allele of <em>Ednrb</em>. In some of these cases, effects of the mutation are easily detected at the transcript level (<em>Tyrp1, Oca2,</em> and <em>Myo5a</em>), but in the other cases (<em>Tyr, Asip, Ednrb,</em> and <em>Kitlg</em>), mutations do not leave a strong imprint on expression.</p>
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