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diff --git a/web/dbdoc/MA_M2_0806_R.html b/web/dbdoc/MA_M2_0806_R.html new file mode 100755 index 00000000..73c4ad6a --- /dev/null +++ b/web/dbdoc/MA_M2_0806_R.html @@ -0,0 +1,2099 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>Kidney Consortium M430v2 July06 RMA</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">Kidney Consortium M430v2 (Aug06) Sex-corrected RMA <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A><BR><BR>Accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=118">GN118</A></P> + + +<P class="subtitle"> Summary:</P> + +<blockquote> +<p>The July 2006 Kidney QTL Consortium data set provides estimates +of mRNA expression in the adult kidney of 70 genetically diverse +strains of mice including 54 BXD recombinant inbred strains, a set +of 15 inbred strains, and 1 F1 hybrid; D2B6F1. Kidney samples were +processed using a total of 153 Affymetrix Mouse Expression 430 2.0 +microarrays (M430v2.0). This particular data set was processed using +the RMA protocol. </p> +</blockquote> + +<P class="subtitle"> About the strains used to generate this set of data:</P> + +<!--BXD42 samples did not pass QC --> + +<blockquote> +<P>The <A HREF="http://www.genenetwork.org/mouseCross.html#BXD" target="_empty" class="fs14">BXD</A> genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 30 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred. We have also included 24 BXD lines generated by Lu and Peirce. All of these strains have been genotyped at 13,377 SNPs. + +<blockquote> +<P><B>Mouse Diversity Panel (MDP)</B>. We have profiled a MDP consisting 15 inbred strains and a pair of F1 hybrids; D2B6F1. These strains were selected for the following reasons: +This panel will be a powerful tool in systems genetic analysis of a wide variety of traits, and will provide additional power in fine mapping modulators through an association analysis of sequence variants. +<UL> +<LI> genetic and phenotypic diversity, including use by the <A 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" class="fs14">Phenome Project</A> +<LI> their use in making genetic reference populations including recombinant inbred strains, cosomic strains, congenic and recombinant congenic strains +<LI> their use by the <A HREF="http://www.complextrait.org" target="_empty" class="fs14">Complex Trait Consortium</A> to make the Collaborative Cross (Nairobi/Wellcome, Oak Ridge/DOE, and Perth/UWA) +<LI> genome sequence data from three sources (NHGRI, Celera, and Perlegen-NIEHS) +<LI> availability from The Jackson Laboratory +</UL> + +<OL> +<LI><A HREF="http://jaxmice.jax.org/strain/002282.html" target="_empty" class="fs14">BTBR T+tf/J</A> +<BR> Multiple recessive stock; Homozygotes show repeated waves of hair loss and regrowth, which begin in the nose and pass posteriorly along the body. + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/C3H.shtml" target="_empty" class="fs14">C3H/HeJ</A> <BR> Sequenced by Perlegen/NIEHS; paternal parent of the BXH panel; Phenome Project A list + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml" target="_empty" class="fs14">C57BL/6J</A> +<BR> Sequenced by NHGRI; parental strain of AXB/BXA, BXD, and BXH; Phenome Project A list + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml" target="_empty" class="fs14">C57BL/6ByJ</A> +<BR> Paternal substrain of B6 used to generate the CXB panel + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/CAST.shtml" target="_empty" class="fs14">CAST/Ei</A> +<BR> Collaborative Cross strain sequenced by NIEHS; Phenome Project A list + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/DBA.shtml" target="_empty" class="fs14">DBA/2J</A> +<BR> Sequenced by Perlegen/NIEHS and Celera; paternal parent of the BXD panel; Phenome Project A list + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/KK.shtml" target="_empty" class="fs14">KK/HlJ</A> +<BR> Sequenced by Perlegen/NIEHS + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/NOD.shtml" target="_empty" class="fs14">NOD/LtJ</A> +<BR> Collaborative Cross strain sequenced by NIEHS; Phenome Project B list; diabetic + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/PWD.shtml" target="_empty" class="fs14">PWD/PhJ</A> +<BR> Sequenced by Perlegen/NIEHS; parental strain for a consomic set by Forjet and colleagues + +<LI><A HREF="http://www.informatics.jax.org/external/festing/mouse/docs/PWK.shtml" target="_empty" class="fs14">PWK/PhJ</A> +<BR> Collaborative Cross strain; Phenome Project D list + +<LI><A HREF=" " target="_empty" class="fs14">WSB/EiJ</A> <BR> Collaborative Cross strain sequenced by NIEHS; Phenome Project C list + +<LI>D2B6F1 +<BR>F1 hybrid generated by crossing C57BL/6J with DBA/2J +</OL> + +<P>These inbred strains can be ordered from The Jackson Laboratory. BXD43 through BXD100 are available from Lu Lu and colleagues at UTHSC. + +</Blockquote> + +</Blockquote> + +<P class="subtitle"> About the animals and tissue used to generate this set of data:</P> + +<Blockquote><P>BXD animals were obtained from UTHSC, and the Jackson Laboratory (Table 1). Animals were housed at UTHSC, at Harvard/BIDMC (Glenn Rosen), at the University of Memphis (Douglas Matthews), or the Jackson Laboratory before sacrifice (see Table 1). Mice were killed by cervical dislocation and kidneys were removed and placed in RNAlater prior to dissection. Kidneys were dissected whole and cleaned from the adrenal glands by Hong Tao Zhang in Dr. Lu’s lab. Kidneys from two to six animals per strain were pooled and shipped to Kremena Star at Mount Sinai School of Medicine (MSSM). Animals used in this study were between 50 and 99 days of age (average of 62 days; see Table 1). +</Blockquote> + +<Blockquote> +<P><B>Sample Processing:</B> : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. +Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols. + +<P><B>Replication and Sample Balance:</B> We obtained a male sample +pool and female sample pool from each isogenic group. Initially +all strains were represented by male and female samples, however, +not all data sets passed the quality control steps. Forty-two (thirty-one +BXD, D2B6F1 and ten inbred strains) are represented by male and +female samples. For the remaining strains, represented by only one +sex we calculated sex-corrected values for each probe set using +the following algorithm: +<p>1. Compute the difference in expression values between the<br> +ALL_FEMALE_AVE and the ALL_MALE_AVE (n = 100 vs n = 52).<br> +b. Divide these values by 2 (additive sex effect) <br> +c. If a female-only strain subtract the "additive sex effect" +<br> +d. If a male-only strain add the "additive sex effect"<br> +</p> +<P><B>Experimental Design and Batch Structure:</B> The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. +All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four. + +</Blockquote> + +<P class="subtitle"> Data Table 1:</P> + +<Blockquote> + +<Blockquote> This table lists all arrays ordered by strain and includes +Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal +Ratio, Percent of transcripts present on the microarray chip, Strain, +Generation, Sex, Age and Source of mice. </Blockquote> +<Blockquote> +<table border="1"> +<tr> +<td>Microarray_ID</td> +<td># mice</td> +<td>Microarray Date</td> +<td>GAPDH (3`/5`)</td> +<td>% present</td> +<td>strains</td> +<td>generation</td> +<td>sex</td> +<td>age</td> +<td>Mice Source</td> +</tr> +<tr> +<td>GKHI-KS-050603.07-051706</td> +<td>3</td> +<td>05/14/02</td> +<td>0.73</td> +<td>37.6</td> +<td>C57BL/6J</td> +<td> </td> +<td>M</td> +<td>56</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-070803.01-051706</td> +<td>3</td> +<td>05/14/02</td> +<td>0.75</td> +<td>41.6</td> +<td>C57BL/6J</td> +<td> </td> +<td>F</td> +<td>69</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-DBA-Male-070706</td> +<td>2</td> +<td>07/06/02</td> +<td>0.71</td> +<td>37.3</td> +<td>DBA/2J</td> +<td> </td> +<td>M</td> +<td>56</td> +<td>JAX</td> +</tr> +<tr> +<td>GKHI_KS_121404.75-042106</td> +<td>4</td> +<td>04/18/02</td> +<td> </td> +<td> </td> +<td>DBA/2J</td> +<td> </td> +<td>F</td> +<td>59</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS_121404.75-033006</td> +<td>4</td> +<td>03/19/02</td> +<td>0.73</td> +<td>48.5</td> +<td>DBA/2J</td> +<td> </td> +<td>F</td> +<td>59</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS_121404.78-042006</td> +<td>4</td> +<td>04/17/02</td> +<td>0.83</td> +<td>40.6</td> +<td>DBA/2J</td> +<td> </td> +<td>F</td> +<td>59</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS_070804.39-042006</td> +<td>4</td> +<td>04/17/02</td> +<td>0.82</td> +<td>39.0</td> +<td>D2B6F1</td> +<td> </td> +<td>M</td> +<td>59</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS_030904.01-042006</td> +<td>4</td> +<td>04/17/02</td> +<td>0.82</td> +<td>35.9</td> +<td>D2B6F1</td> +<td> </td> +<td>M</td> +<td>57</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-121404.73-070706</td> +<td>2</td> +<td>07/06/02</td> +<td>0.76</td> +<td>36.3</td> +<td>D2B6F1</td> +<td> </td> +<td>F</td> +<td>69</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-010705.38-051206</td> +<td>5</td> +<td>05/09/02</td> +<td>0.81</td> +<td>39.9</td> +<td>BXD1</td> +<td> </td> +<td>M</td> +<td>59</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-060905.19</td> +<td>5</td> +<td>06/05/02</td> +<td>0.75</td> +<td>42.3</td> +<td>BXD1</td> +<td> </td> +<td>M</td> +<td>68</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-051206.13-070706</td> +<td>3</td> +<td>07/06/02</td> +<td>0.71</td> +<td>36.3</td> +<td>BXD1</td> +<td> </td> +<td>F</td> +<td>57</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-021304.10-051206</td> +<td>4</td> +<td>05/09/02</td> +<td>0.81</td> +<td>39.1</td> +<td>BXD2</td> +<td> </td> +<td>M</td> +<td>61</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-040303-04-050406</td> +<td>3</td> +<td>05/01/02</td> +<td>0.80</td> +<td>37.6</td> +<td>BXD5</td> +<td> </td> +<td>F</td> +<td>56</td> +<td>UMemphis</td> +</tr> +<tr> +<td>GKHI-KS-010705-53-050306</td> +<td>5</td> +<td>05/01/02</td> +<td>0.76</td> +<td>37.1</td> +<td>BXD5</td> +<td> </td> +<td>F</td> +<td>58</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-031103.01-062206</td> +<td>3</td> +<td>06/21/02</td> +<td>0.75</td> +<td>37.1</td> +<td>BXD5</td> +<td> </td> +<td>M</td> +<td>71</td> +<td>UMemphis</td> +</tr> +<tr> +<td>GKHI-KS-040505-51-050306</td> +<td>5</td> +<td>05/01/02</td> +<td>0.71</td> +<td>35.5</td> +<td>BXD6</td> +<td> </td> +<td>M</td> +<td>58</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-092705-29--050406</td> +<td>5</td> +<td>05/02/02</td> +<td>0.75</td> +<td>36.1</td> +<td>BXD6</td> +<td>160</td> +<td>F</td> +<td>64</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS_092404.01-042106</td> +<td>4</td> +<td>04/18/02</td> +<td>0.71</td> +<td>36.3</td> +<td>BXD8</td> +<td> </td> +<td>M</td> +<td>59</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-051205-25-042706</td> +<td>5</td> +<td>04/23/02</td> +<td>0.92</td> +<td>37.9</td> +<td>BXD8</td> +<td> </td> +<td>F</td> +<td>77</td> +<td>UTM RW</td> +</tr> +<tr> +<td>KS-021605-17-042606</td> +<td>5</td> +<td>04/22/02</td> +<td>0.85</td> +<td>40.8</td> +<td>BXD9</td> +<td> </td> +<td>F</td> +<td>67</td> +<td>UTM RW</td> +</tr> +<tr> +<td>KS-032905-32-042606</td> +<td>5</td> +<td>04/22/02</td> +<td>0.91</td> +<td>36.8</td> +<td>BXD9</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-062006.08-070706</td> +<td>3</td> +<td>07/06/02</td> +<td>0.74</td> +<td>36.3</td> +<td>BXD9</td> +<td> </td> +<td>M</td> +<td>78</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-031505.22-051206</td> +<td>5</td> +<td>05/09/02</td> +<td>0.74</td> +<td>39.5</td> +<td>BXD11</td> +<td> </td> +<td>F</td> +<td>65</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-031605.01</td> +<td>5</td> +<td>06/05/02</td> +<td>0.74</td> +<td>43.4</td> +<td>BXD11</td> +<td> </td> +<td>F</td> +<td>69</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS_102104.40-042106</td> +<td>4</td> +<td>04/18/02</td> +<td>0.72</td> +<td>38.5</td> +<td>BXD12</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-112002.07-051106</td> +<td>2</td> +<td>05/08/02</td> +<td>0.77</td> +<td>42.0</td> +<td>BXD12</td> +<td> </td> +<td>F</td> +<td>64</td> +<td>UMemphis</td> +</tr> +<tr> +<td>GKHI-KS-120904.33-051206</td> +<td>4</td> +<td>05/09/02</td> +<td>0.71</td> +<td>38.4</td> +<td>BXD13</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-042304.01</td> +<td>4</td> +<td>06/05/02</td> +<td>0.71</td> +<td>44.1</td> +<td>BXD13</td> +<td> </td> +<td>F</td> +<td>58</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-020905.34-051106</td> +<td>5</td> +<td>05/08/02</td> +<td>0.75</td> +<td>40.7</td> +<td>BXD14</td> +<td> </td> +<td>F</td> +<td>68</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-022405.46-051106</td> +<td>5</td> +<td>05/08/02</td> +<td>0.71</td> +<td>40.2</td> +<td>BXD14</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-091704.09-062206</td> +<td>4</td> +<td>06/21/02</td> +<td>0.73</td> +<td>39.0</td> +<td>BXD14</td> +<td> </td> +<td>M</td> +<td>59</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-013004.45-062206</td> +<td>4</td> +<td>06/21/02</td> +<td>0.76</td> +<td>38.5</td> +<td>BXD15</td> +<td> </td> +<td>M</td> +<td>61</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-022405.43-051106</td> +<td>5</td> +<td>05/08/02</td> +<td>0.73</td> +<td>40.5</td> +<td>BXD15</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-041604.10-051106</td> +<td>4</td> +<td>05/08/02</td> +<td>0.73</td> +<td>42.6</td> +<td>BXD15</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-031805.01-051106</td> +<td>5</td> +<td>05/08/02</td> +<td>0.79</td> +<td>42.4</td> +<td>BXD16</td> +<td> </td> +<td>F</td> +<td>59</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-031805.04-051106</td> +<td>5</td> +<td>05/08/02</td> +<td>0.77</td> +<td>39.9</td> +<td>BXD16</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-040805.10-051006</td> +<td>5</td> +<td>05/05/02</td> +<td>0.93</td> +<td>38.7</td> +<td>BXD18</td> +<td> </td> +<td>F</td> +<td>59</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-052804.09-051106</td> +<td>4</td> +<td>05/05/02</td> +<td>0.67</td> +<td>37.6</td> +<td>BXD19</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-010705.47-051106</td> +<td>5</td> +<td>05/05/02</td> +<td>0.73</td> +<td>42.3</td> +<td>BXD19</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-010705.44-070706</td> +<td>3</td> +<td>07/06/02</td> 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+<td>04/03/02</td> +<td>0.77</td> +<td>38.3</td> +<td>BXD69</td> +<td>20</td> +<td>F</td> +<td>63</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-042705-01-042706</td> +<td>5</td> +<td>04/23/02</td> +<td>0.83</td> +<td>38.6</td> +<td>BXD70</td> +<td>21</td> +<td>F</td> +<td>64</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-051705-59-042706</td> +<td>5</td> +<td>04/23/02</td> +<td>0.89</td> +<td>38.5</td> +<td>BXD70</td> +<td>22</td> +<td>F</td> +<td>61</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-030805-40-042706</td> +<td>5</td> +<td>04/23/02</td> +<td>0.86</td> +<td>38.5</td> +<td>BXD73</td> +<td>23</td> +<td>F</td> +<td>61</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-041905.172-062206</td> +<td>5</td> +<td>06/21/02</td> +<td>0.79</td> +<td>37.6</td> +<td>BXD73</td> +<td>24</td> +<td>M</td> +<td>64</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-072605-03-042706</td> +<td>5</td> +<td>04/23/02</td> +<td>0.87</td> +<td>38.2</td> +<td>BXD73</td> +<td>25</td> +<td>F</td> +<td>72</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-041205-04-050406</td> +<td>5</td> +<td>05/02/02</td> +<td>0.83</td> +<td>41.4</td> +<td>BXD75</td> +<td>22</td> +<td>F</td> +<td>60</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-041205.07</td> +<td>5</td> +<td>06/05/02</td> +<td>0.79</td> +<td>45.8</td> +<td>BXD75</td> +<td>22</td> +<td>F</td> +<td>60</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-101805-35-050406</td> +<td>5</td> +<td>05/02/02</td> +<td>0.79</td> +<td>38.4</td> +<td>BXD77</td> +<td>24</td> +<td>F</td> +<td>60</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-070605.43</td> +<td>5</td> +<td>06/05/02</td> +<td>0.77</td> +<td>42.8</td> +<td>BXD77</td> +<td>23</td> +<td>F</td> +<td>62</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-071205-31-042706</td> +<td>5</td> +<td>04/23/02</td> +<td>0.91</td> +<td>37.7</td> +<td>BXD80</td> +<td>20</td> +<td>F</td> +<td>65</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-071205-2-042706</td> +<td>5</td> +<td>04/23/02</td> +<td>0.90</td> +<td>38.1</td> +<td>BXD80</td> +<td>20</td> +<td>F</td> +<td>65</td> +<td>UTM RW</td> +</tr> +<tr> +<td>KS-011305-11-042606</td> +<td>5</td> +<td>04/22/02</td> +<td>0.82</td> +<td>39.0</td> +<td>BXD85</td> +<td>22</td> +<td>M</td> +<td>91</td> +<td>UTM RW</td> +</tr> +<tr> +<td>KS-110805-27-042606</td> +<td>5</td> +<td>04/22/02</td> +<td>0.91</td> +<td>35.2</td> +<td>BXD85</td> +<td>25</td> +<td>F</td> +<td>63</td> +<td>UTM RW</td> +</tr> +<tr> +<td>KS-080404-28-042606</td> +<td>4</td> +<td>04/22/02</td> +<td>0.84</td> +<td>36.8</td> +<td>BXD86</td> +<td>21</td> +<td>F</td> +<td>58</td> +<td>UTM RW</td> +</tr> +<tr> +<td>KS-080504-04-042606</td> +<td>4</td> +<td>04/22/02</td> +<td>0.81</td> +<td>33.4</td> +<td>BXD86</td> +<td>20</td> +<td>M</td> +<td>77</td> +<td>UTM RW</td> +</tr> +<tr> +<td>KS-051705-57-042606</td> +<td>5</td> +<td>04/22/02</td> +<td>1.11</td> +<td>35.6</td> +<td>BXD87</td> +<td>20</td> +<td>M</td> +<td>63</td> +<td>UTM RW</td> +</tr> +<tr> +<td>KS-032905-46-042606</td> +<td>5</td> +<td>04/22/02</td> +<td>0.85</td> +<td>36.1</td> +<td>BXD87</td> +<td>20</td> +<td>M</td> +<td>57</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-080905-49-042706</td> +<td>5</td> +<td>04/23/02</td> +<td>0.89</td> +<td>37.6</td> +<td>BXD90</td> +<td>23</td> +<td>F</td> +<td>71</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-101105.26</td> +<td>5</td> +<td>06/05/02</td> +<td>0.84</td> +<td>43.6</td> +<td>BXD90</td> +<td>25</td> +<td>F</td> +<td>70</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS-062304.02-040606</td> +<td>4</td> +<td>04/03/02</td> +<td>0.85</td> +<td>40.9</td> +<td>BXD92</td> +<td>21</td> +<td>M</td> +<td>55</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS_071404.01-042006</td> +<td>4</td> +<td>04/17/02</td> +<td>0.77</td> +<td>39.5</td> +<td>BXD92</td> +<td>21</td> +<td>F</td> +<td>62</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI_KS_031005.17-042006</td> +<td>5</td> +<td>04/17/02</td> +<td>0.77</td> +<td>38.1</td> +<td>BXD96</td> +<td>20</td> +<td>M</td> +<td>65</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-111505.12</td> +<td>5</td> +<td>06/05/02</td> +<td>0.77</td> +<td>44.1</td> +<td>BXD96</td> +<td>23</td> +<td>M</td> +<td>66</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-012406.21-060806</td> +<td>3</td> +<td>06/07/02</td> +<td>0.73</td> +<td>36.6</td> +<td>BTBR T+tf/J</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-012406.24-060806</td> +<td>3</td> +<td>06/07/02</td> +<td>1.28</td> +<td>39.2</td> +<td>BTBR T+tf/J</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-030206.13-060806</td> +<td>3</td> +<td>06/07/02</td> +<td>0.71</td> +<td>41.2</td> +<td>BXSB/MpJ</td> +<td> </td> +<td>F</td> +<td>61</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-030206.16-060806</td> +<td>3</td> +<td>06/07/02</td> +<td>0.66</td> +<td>37.2</td> +<td>BXSB/MpJ</td> +<td> </td> +<td>F</td> +<td>61</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-011906.31-060806</td> +<td>3</td> +<td>06/07/02</td> +<td>0.80</td> +<td>37.2</td> +<td>C3H/HeJ</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-011906.34-060806</td> +<td>3</td> +<td>06/07/02</td> +<td>0.76</td> +<td>38.5</td> +<td>C3H/HeJ</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-060806.04-070706</td> +<td>3</td> +<td>07/06/02</td> +<td>0.68</td> +<td>37.3</td> +<td>C3H/HeJ</td> +<td> </td> +<td>F</td> +<td>76</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-071505.08-060806</td> +<td>3</td> +<td>06/07/02</td> +<td>0.71</td> +<td>37.4</td> +<td>C57BL/6ByJ</td> +<td> </td> +<td>F</td> +<td>51</td> +<td>JAX</td> +</tr> +<tr> +<td>GKHI-KS-071505.11-060806</td> +<td>2</td> +<td>06/07/02</td> +<td>0.73</td> +<td>39.2</td> +<td>C57BL/6ByJ</td> +<td> </td> +<td>F</td> +<td>51</td> +<td>JAX</td> +</tr> +<tr> +<td>GKHI-KS-030305.15-060806</td> +<td>3</td> +<td>06/07/02</td> +<td>0.71</td> +<td>37.4</td> +<td>CAST/Ei</td> +<td> </td> +<td>F</td> +<td>64</td> +<td>JAX</td> +</tr> +<tr> +<td>GKHI-KS-031005.35-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.70</td> +<td>35.7</td> +<td>CAST/Ei</td> +<td> </td> +<td>M</td> +<td>64</td> +<td>JAX</td> +</tr> +<tr> +<td>GKHI-KS-022206.16-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.71</td> +<td>37.9</td> +<td>KK/HlJ</td> +<td> </td> +<td>F</td> +<td>61</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-022206.07-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.72</td> +<td>35.5</td> +<td>KK/HlJ</td> +<td> </td> +<td>M</td> +<td>61</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-031606.01-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.86</td> +<td>35.9</td> +<td>MOLF/Ei</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-022206.16-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.87</td> +<td>37.4</td> +<td>MOLF/Ei</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-012006.25-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.75</td> +<td>38.3</td> +<td>NOD/LtJ</td> +<td> </td> +<td>F</td> +<td>58</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-012006.28-061306</td> +<td>3</td> +<td>06/11/02</td> +<td>0.82</td> +<td>37.1</td> +<td>NOD/LtJ</td> +<td> </td> +<td>F</td> +<td>58</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-032306.04.060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.73</td> +<td>40.2</td> +<td>NZB/BlNJ</td> +<td> </td> +<td>F</td> +<td>61</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-032306.07-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.74</td> +<td>39.4</td> +<td>NZB/BlNJ</td> +<td> </td> +<td>F</td> +<td>61</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-020706.04-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.71</td> +<td>41.6</td> +<td>NZW/LacJ</td> +<td> </td> +<td>F</td> +<td>65</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-020206.19-060906</td> +<td>3</td> +<td>06/08/02</td> +<td>0.77</td> +<td>36.7</td> +<td>NZW/LacJ</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-012406.33-061306</td> +<td>3</td> +<td>06/11/02</td> +<td>0.95</td> +<td>35.3</td> +<td>PWD/PhJ</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-012406.30-062006</td> +<td>3</td> +<td>06/18/02</td> +<td>0.88</td> +<td>36.3</td> +<td>PWD/PhJ</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-020206.01-062206</td> +<td>3</td> +<td>06/21/02</td> +<td>1.02</td> +<td>35.9</td> +<td>PWK/PhJ</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-020206.04-062206</td> +<td>3</td> +<td>06/21/02</td> +<td>0.96</td> +<td>38.7</td> +<td>PWK/PhJ</td> +<td> </td> +<td>F</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-020206.07-062206</td> +<td>3</td> +<td>06/21/02</td> +<td>0.98</td> +<td>36.6</td> +<td>PWK/PhJ</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-020206.10-062206</td> +<td>3</td> +<td>06/21/02</td> +<td>0.87</td> +<td>35.2</td> +<td>PWK/PhJ</td> +<td> </td> +<td>M</td> +<td>60</td> +<td>Harvard/BIDMC </td> +</tr> +<tr> +<td>GKHI-KS-052705.01-061306</td> +<td>2</td> +<td>06/11/02</td> +<td>0.72</td> +<td>38.3</td> +<td>WSB/EiJ</td> +<td> </td> +<td>F</td> +<td>52</td> +<td>UTM RW</td> +</tr> +<tr> +<td>GKHI-KS-051005.07-061306</td> +<td>3</td> +<td>06/11/02</td> +<td>0.77</td> +<td>38.0</td> +<td>WSB/EiJ</td> +<td> </td> +<td>M</td> +<td>58</td> +<td>JAX</td> +</tr> +</table> +</Blockquote> +</Blockquote> + + +<P class="subtitle"> Downloading all data:</P> +<Blockquote> +<P>All data links (right-most column above) will be made active as sooon as the global analysis of these data by the Consoritum has been accepted for publication. Please see text on <A HREF="http://www.genenetwork.org/dataSharing.html" target="_empty" class="fs14">Data Sharing Policies</A>, and <A HREF="http://www.genenetwork.org/conditionsofUse.html" target="_empty" class="fs14">Conditions and Limitations</A>, and <A HREF="http://www.genenetwork.org/statusandContact.html" target="_empty" class="fs14">Contacts</A>. Following publication, download a summary text file or Excel file of the PDNN probe set data. Contact RW Williams regarding data access problems. +</P> +</Blockquote> + + + + +<P class="subtitle"> About the array platform:</P> +<Blockquote> +<P><B>Affymetrix Mouse Genome 430 2.0 array: </B>The <A HREF="http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20" target="_blank" class="fs14">430v2</A> array consists of 992936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts and the majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using Unigene Build 107 by Affymetrix. The UTHSC group has recently reannotated all probe sets on this array, producing more accurate data on probe and probe set targets. All probes were aligned to the most recent assembly of the Mouse Genome (Build 34, mm6) using Jim Kent's BLAT program. Many of the probe sets have been manually curated by Jing Gu and Rob Williams. </P> +</Blockquote> + +<P class="subtitle"> About data processing:</P> + +<Blockquote> + +<P><B>Probe set data from the CHP file: </B>The expression values were generated using RMA. The same simple steps described above were also applied to these values. </Blockquote> + +<Blockquote> +<P>Probe level QC: Log2 probe data of all arrays were inspected in DataDesk. Inspection involved examining scatterplots of pairs of arrays for signal homogeneity (i.e., high correlation and linearity of the bivariate plots) and looking at all pairs of correlation coefficients. + +<P>Validation of strains and sex of each array data set: A subset of probes and probe sets with a Mendelian pattern of inheritance were used to construct a expression correlation matrix for all arrays and the ideal Mendelian expectation for each strain constructed from the genotypes. There should naturally be a very high correlation in the expression patterns of transcripts with Mendelian phenotypes within each strain, as well as with the genotype strain distribution pattern of markers for the strain. + +<P>Sex of the samples was validated using sex-specific probe sets such as <I>Xist</I> and <I>Dby</I>. + +</Blockquote> + + +<P class="subtitle"> Data source acknowledgment:</P> +<Blockquote><P>Data were generated with funds provided by a variety of public and private source to members of the Kidney Consortium. Members of the Kidney Consortium thank the following sources for financial support of this effort: + +<UL> +<LI>Erwin P. Bottinger, M.D. <br> +Grant Support: R01 DK60043-04 <br> +<LI>Russell W. Chesney, M.D. <br> +Grant Support: Le Bonheur Chair of Excellence in Pediatrics II +<br> +<LI>Lu Lu, M.D. <br> +Grant Support: NIH U01AA13499, U24AA13513 <br> +<LI>Peter Mundel <br> +Grant Support: NIH R01DK57683, NIH R01 DK 62472 <br> +<LI>Paul E. Klotman <br> +Grant Support: PO1 DK56492, PO1 DK56492. <br> +<LI> Matthew D. Breyer <br> +Grant Support: DK-38226 <br> +<LI>Kenneth F. Manly, Ph.D. <br> +Grant Support: NIH P20MH062009 and U01CA105417 <br> +<LI>Robert W. Williams, Ph.D. <br> +Grant Support: NIH U01AA013499, P20MH062009, U01AA013499, U01AA013513 +</UL> + + +</P></Blockquote> + +<P class="subtitle"> About this text file:</P> +<Blockquote><P> +This text file originally generated by Kremena Star on Sept. 1, 2006. +</P></Blockquote> + + + + +<P></P> + +</TD> +</TR> +<TR> +<TD colspan=2 align=center bgColor=#ddddff> + + + +<!--Start of footer--> +<TABLE width="90%"> +<script language='JavaScript' src='/javascript/footer.js'></script> +</TABLE> +<!--End of footer--> + + + +</TD> +</TR> +</TABLE><!-- /Footer --> + +<!-- menu script itself. you should not modify this file --> +<script language="JavaScript" src="/javascript/menu_new.js"></script> +<!-- items structure. menu hierarchy and links are stored there --> +<script language="JavaScript" src="/javascript/menu_items.js"></script> + +<!-- files with geometry and styles structures --> +<script language="JavaScript" src="/javascript/menu_tpl.js"></script> +<script language="JavaScript"> +<!--// +// Note where menu initialization block is located in HTML document. +// Don't try to position menu locating menu initialization block in +// some table cell or other HTML element. 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