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diff --git a/web/dbdoc/LV_G_0704_ABF.html b/web/dbdoc/LV_G_0704_ABF.html new file mode 100755 index 00000000..a0ffa726 --- /dev/null +++ b/web/dbdoc/LV_G_0704_ABF.html @@ -0,0 +1,329 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>UNC Agilent G4121A Liver Database (July/04 Freeze) AFE v6.1 / WebQTL</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="5" topmargin="5" leftmargin="5" rightmargin="5" marginheight="5" marginwidth="5" text=#000000 bgColor=#ffffff> +<TABLE cellSpacing=3 cellPadding=4 width="100%" border=0> + <TBODY> + <TR> + <script language="JavaScript" src="/javascript/header.js"></script> + </TR> + <TR> + <!-- Body Start from Here --> + <TD vAlign=top width="100%" colspan=2 bgColor=#eeeeee> + <P class="title">UNC Agilent G4121A Liver Database (Jul04 Freeze) Agilent FE v6.1 <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> + + +<P class="subtitle"> Summary:</P> + +<Blockquote> +This data set provides estimates of mRNA expression in livers of 38 adult BXD recombinant inbred mice measured using Agilent G4121A microarray. Data were generated as part of the NIEHS Toxicogenomics Research Consortium program at the University of North Carolina at Chapel Hill (Akira Maki, David Threadgill, and Ivan Rusyn) and by the Informatics Center for Mouse Neurogenetics at the University of Tennessee Heath Science Center (Lu Lu, Elissa Chesler, Yanhua Qu, Kenneth Manly, and Robert Williams). Data were processed using Agilent's feature extraction (FE) software version 6.1. This is the first data freeze. For background on the NIEHS Toxicogenomics Research Consortium and the Chemical Effects in Biological Systems (CEBS) program please link to a <A HREF="http://www.unc.edu/courses/2004spring/envr/132/001/4_6_04_handout.pdf" target="_blank" class="normal">PDF</A> by Michael D. Waters. + +</Blockquote> + + +<P class="subtitle"> About the cases used to generate this set of data:</P> + +<Blockquote>Ninety-six BXD liver sample pools were obtained from animals reared at UTHSC in a pathogen-free vivarium. Mice were experimentally naive and housed at weaning (20 to 24 days-of-age) in same-sex groups in standard mouse shoebox cages. Mice were 56 to 177 days old at the time of sacrifice. Thirty-eight mouse strains were used of which 27 were represented by both sexes.</Blockquote> + + <Blockquote> + <table border="0" cellpadding="0" cellspacing="0" bgcolor="#000000" width="60%" align="Center"> + <tr> + <td> + <table width="100%" border="0" cellpadding="5" cellspacing="1"> + <tr bgcolor="royalblue"><td><font color=#FFFFFF>Strain Name</font></td> + <td><font color=#FFFFFF><center>Sex</center></font></td> + <td><font color=#FFFFFF><center>WebQTL Strain ID</center></font></td></tr> +<tr bgcolor="#eeeeee"><td>C57BL/6J</td><td><center>M and F</center></td><td><center>C57BL/6J</center></td></tr> +<tr bgcolor="#eeeeee"><td>DBA/2J</td><td><center>M and F</center></td><td><center>DBA/2J</center></td></tr> +<tr bgcolor="#eeeeee"><td>B6D2F1</td><td><center>M and F</center></td><td><center>F1</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD1</td><td><center>M and F</center></td><td><center>BXD1</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD2</td><td><center>F</center></td><td><center>BXD2</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD5</td><td><center>M and F</center></td><td><center>BXD5</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD6</td><td><center>M and F</center></td><td><center>BXD6</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD8</td><td><center>F</center></td><td><center>BXD8</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD9</td><td><center>M and F</center></td><td><center>BXD9</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD11</td><td><center>M</Center></td><td><center>BXD11</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD12</td><td><center>M and F</center></td><td><center>BXD12</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD13</td><td><center>M and F</center></td><td><center>BXD13</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD14</td><td><center>M</center></td><td><center>BXD14</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD15</td><td><center>M and F</center></td><td><center>BXD15</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD21</td><td><center>M and F</center></td><td><center>BXD21</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD23</td><td><center>M</center></td><td><center>BXD23</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD24</td><td><center>M and F</center></td><td><center>BXD24</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD28</td><td><center>M and F</center></td><td><center>BXD28</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD29</td><td><center>M and F</center></td><td><center>BXD29</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD31</td><td><center>M and F</center></td><td><center>BXD31</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD32</td><td><center>F</center></td><td><center>BXD32</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD33</td><td><center>F (?)</center></td><td><center>BXD33</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD34</td><td><center>M and F</center></td><td><center>BXD34</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD36</td><td><center>M and F (?)</center></td><td><center>BXD36</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD38</td><td><center>M and F</center></td><td><center>BXD38</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD39</td><td><center>M and F</center></td><td><center>BXD39</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD40</td><td><center>M and F</center></td><td><center>BXD40</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD42</td><td><center>M and F</center></td><td><center>BXD42</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD43</td><td><center>M and F</center></td><td><center>BXD43</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD44</td><td><center>M and F</center></td><td><center>BXD44</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD45</td><td><center>F</center></td><td><center>BXD45</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD48</td><td><center>M</center></td><td><center>BXD48</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD51</td><td><center>F (?)</center></td><td><center>BXD51</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD60</td><td><center>M and F</center></td><td><center>BXD60</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD62</td><td><center>M and F (?)</center></td><td><center>BXD62</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD77</td><td><center>M and F</center></td><td><center>BXD77</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD85</td><td><center>M and F (?)</center></td><td><center>BXD85</center></td></tr> +<tr bgcolor="#eeeeee"><td>BXD86</td><td><center>F (?)</center></td><td><center>BXD86</center></td></tr> + </table> + </td> + </tr> + </table> + </Blockquote> + +<Blockquote> +C57BL/6J, DBA/2J, and BXD1 through BXD42 were originally obtained from The Jackson Laboratory. Advanced intercross BXD strains (BXD43 and higher) were generated at Princeton University and UTHSC (Peirce and Lu, <A href="http://www.biomedcentral.com/1471-2156/5/7" class="normal" target="_Blank" >2004</A>). All of these new strains were inbred for at least 14 generations. + </Blockquote> + + + <P class="subtitle"> About the tissue used to generate these data:</P> + <Blockquote><P>Animals were killed by cervical dislocation. The entire liver was removed within less than 5 minutes by Zhiping Jia or Hongtao Zhai and placed in RNAlater (Ambion) overnight at 4 degrees. Tissue was stored in single vials (2 to 3 cases per vial) at -80 degrees. Tissue vials were shipped to UNC on ice by FedEX. Prior to isolation of RNA, liver samples from the same strain and sex (2 to 3 animals) were pooled in equal amount and minced in a homogenization buffer using an electric homogenizer. Total RNA was isolated using Qiagen RNeasy Mini kits according to the manufacturer's instructions. RNA purity and quality were verified using a BioAnalyzer 2100 and Low RNA Input Linear Amplification kits (Agilent Technologies, Wilmington, DE) in these experiments. RNA labeling, array hybridization and washing and other procedures were performed according to the manufacturer's protocols. A common reference design was used. Male C57BL/6J mouse pooled (equal amounts of RNA from liver, kidney, lung, brain and spleen) RNA provided by the Toxicogenomics Research Consortium was used as a common reference in all these experiments. + </P></Blockquote> + +<P class="subtitle"> About the array platform</P> + + <Blockquote>Samples were assayed using <A HREF="http://www.chem.agilent.com/scripts/generic.asp?lPage=10408&indcol=Y&prodcol=Y" target="_Blank" class="normal"> G4121A</A> Agilent oligomer microarray glass slides (1" x 3" format). This microarray estimate expression of approximately 20,842 mouse genes, including a special set of toxicology transcripts nominated by a collaboration that included the National Institute of Environmental Health Sciences (NIEHS) and members of the Toxicogenomics Research Consortium. + </Blockquote> + <Blockquote> + <table border="0" cellpadding="0" cellspacing="0" bgcolor="#000000" width="85%" align="Center"> + <tr> + <td><center> + <table width="100%" border="0" cellpadding="5" cellspacing="1"> + <tr bgcolor="royalblue"><td><center><font color=#FFFFFF>Experiment ID</font></center></td> + <td><center><font color=#FFFFFF>Experiment Name</font></center></td> + <td><center><font color=#FFFFFF>Batch#</font></center></td> + <td><center><font color=#FFFFFF>Sample ID</font></center></td> + <td><center><font color=#FFFFFF>Strain</font></center></td> + <td><center><font color=#FFFFFF>Sex</font></center></td> + <td><center><font color=#FFFFFF>Array Barcode#</font></center></td></tr> + <tr bgcolor="#eeeeee"><td><center>35781</center></td><td><center>C57BL/6J M B1</center></td><td><center>1</center></td><td><center>614</center></td><td><center>C57BL/6J</center></td><td><center>M</center></td><td><center>251197818088</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35780</center></td><td><center>C57BL/6J M B1R</center></td><td><center>1</center></td><td><center>614</center></td><td><center>C57BL/6J</center></td><td><center>M</center></td><td><center>251197817961</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35782</center></td><td><center>C57BL/6J F B1</center></td><td><center>1</center></td><td><center>5</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197818089</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35783</center></td><td><center>DBA/2J F B1</center></td><td><center>1</center></td><td><center>1</center></td><td><center>DBA/2J</center></td><td><center>F</center></td><td><center>251197818090</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35768</center></td><td><center>B6D2F1 M B1</center></td><td><center>1</center></td><td><center>609</center></td><td><center>B6D2F1</center></td><td><center>M</center></td><td><center>251197817934</center></td></tr> + + +<!-- RWW: Changed sex to "unknown", per Lu Lu's analysis of Nov 16, 2004. Regenotyping of these cases confirms that they are all males. However, the expression of Eif2s3x and AI314753 (female markers) and Ddx3y and Uty (male markers) indicates that the samples are female. Given the discrepancy between genotypes at UT and sample sex at UNC, mishandling of sample 96 is a possible explanation.--> + +<tr bgcolor="#eeeeee"><td><center>35769</center></td><td><center>B6D2F1 F B1</center></td><td><center>1</center></td><td><center>96</center></td><td><center>B6D2F1</center></td><td><center>Unknown</center></td><td><center>251197817935</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35770</center></td><td><center>BXD1 M</center></td><td><center>1</center></td><td><center>9</center></td><td><center>BXD1</center></td><td><center>M</center></td><td><center>251197817936</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35771</center></td><td><center>BXD12 F</center></td><td><center>1</center></td><td><center>13</center></td><td><center>BXD12</center></td><td><center>F</center></td><td><center>251197817937</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35772</center></td><td><center>BXD23 M</center></td><td><center>1</center></td><td><center>24</center></td><td><center>BXD23</center></td><td><center>M</center></td><td><center>251197817938</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35773</center></td><td><center>BXD34 F</center></td><td><center>1</center></td><td><center>43</center></td><td><center>BXD34</center></td><td><center>F</center></td><td><center>251197817939</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35774</center></td><td><center>BXD28 M</center></td><td><center>1</center></td><td><center>29</center></td><td><center>BXD28</center></td><td><center>M</center></td><td><center>251197817940</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35775</center></td><td><center>BXD29 F</center></td><td><center>1</center></td><td><center>30</center></td><td><center>BXD29</center></td><td><center>F</center></td><td><center>251197817941</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35776</center></td><td><center>BXD39 M</center></td><td><center>1</center></td><td><center>54</center></td><td><center>BXD39</center></td><td><center>M</center></td><td><center>251197817942</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35777</center></td><td><center>BXD40 F</center></td><td><center>1</center></td><td><center>59</center></td><td><center>BXD40</center></td><td><center>F</center></td><td><center>251197817943</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35778</center></td><td><center>BXDA10 M</center></td><td><center>1</center></td><td><center>500</center></td><td><center>BXD77</center></td><td><center>M</center></td><td><center>251197817959</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35779</center></td><td><center>BXD8 F</center></td><td><center>1</center></td><td><center>613</center></td><td><center>BXD8</center></td><td><center>F</center></td><td><center>251197817960</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35509</center></td><td><center>C57BL/6J M B2</center></td><td><center>2</center></td><td><center>8</center></td><td><center>C57BL/6J </center></td><td><center>M</center></td><td><center>251197818158</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35529</center></td><td><center>C57BL/6J M B2R</center></td><td><center>2</center></td><td><center>8</center></td><td><center>C57BL/6J </center></td><td><center>M</center></td><td><center>251197818086</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35578</center></td><td><center>C57BL/6J F B2</center></td><td><center>2</center></td><td><center>5</center></td><td><center>C57BL/6J </center></td><td><center>F</center></td><td><center>251197818159</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35535</center></td><td><center>DBA/2J F B2</center></td><td><center>2</center></td><td><center>1</center></td><td><center>DBA/2J </center></td><td><center>F</center></td><td><center>251197818160</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35536</center></td><td><center>DBA/2J M B2</center></td><td><center>2</center></td><td><center>4</center></td><td><center>DBA/2J </center></td><td><center>M</center></td><td><center>251197818161</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35537</center></td><td><center>DBA/2J F B2(3)</center></td><td><center>2</center></td><td><center>3</center></td><td><center>DBA/2J </center></td><td><center>F</center></td><td><center>251197818162</center></td></tr> + +<!-- RWW: Changed sex to 2 females and 1 male, per Lu Lu regenotyping of these cases.--> +<tr bgcolor="#eeeeee"><td><center>35538</center></td><td><center>C57BL/6J F B2(7)</center></td><td><center>2</center></td><td><center>7</center></td><td><center>C57BL/6J </center></td><td><center>2F, 1M</center></td><td><center>251197818163</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35528</center></td><td><center>B6D2F1 M</center></td><td><center>2</center></td><td><center>603</center></td><td><center>B6D2F1 </center></td><td><center>M</center></td><td><center>251197818084</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35539</center></td><td><center>B6D2F1 F</center></td><td><center>2</center></td><td><center>601</center></td><td><center>B6D2F1 </center></td><td><center>F</center></td><td><center>251197818177</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35540</center></td><td><center>BXD11 M</center></td><td><center>2</center></td><td><center>12</center></td><td><center>BXD11</center></td><td><center>M</center></td><td><center>251197818178</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35541</center></td><td><center>BXD13 F</center></td><td><center>2</center></td><td><center>16</center></td><td><center>BXD13 </center></td><td><center>F</center></td><td><center>251197818179</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35542</center></td><td><center>BXD21 M</center></td><td><center>2</center></td><td><center>21</center></td><td><center>BXD21</center></td><td><center>M</center></td><td><center>251197818180</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35543</center></td><td><center>BXD24 F</center></td><td><center>2</center></td><td><center>25</center></td><td><center>BXD24</center></td><td><center>F</center></td><td><center>251197818181</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35514</center></td><td><center>BXD31 M</center></td><td><center>2</center></td><td><center>34</center></td><td><center>BXD31</center></td><td><center>M</center></td><td><center>251197817944</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35515</center></td><td><center>BXD32 F</center></td><td><center>2</center></td><td><center>36</center></td><td><center>BXD32</center></td><td><center>F</center></td><td><center>251197817945</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35516</center></td><td><center>BXD42 M</center></td><td><center>2</center></td><td><center>63</center></td><td><center>BXD42</center></td><td><center>M</center></td><td><center>251197817946</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35517</center></td><td><center>BXD5 F</center></td><td><center>2</center></td><td><center>65</center></td><td><center>BXD5</center></td><td><center>F</center></td><td><center>251197817947</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35527</center></td><td><center>BXDAP15 M</center></td><td><center>2</center></td><td><center>79</center></td><td><center>BXD62</center></td><td><center>M</center></td><td><center>251197817948</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35531</center></td><td><center>BXDAP19 F</center></td><td><center>2</center></td><td><center>81</center></td><td><center>BXD43</center></td><td><center>F</center></td><td><center>251197818085</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35916</center></td><td><center>C57BL/6J M B3</center></td><td><center>3</center></td><td><center>506</center></td><td><center>C57BL/6J</center></td><td><center>M</center></td><td><center>251197817964</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35932</center></td><td><center>C57BL/6J M B3R</center></td><td><center>3</center></td><td><center>506</center></td><td><center>C57BL/6J</center></td><td><center>M</center></td><td><center>16011978011862</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35917</center></td><td><center>DBA/2J M B3</center></td><td><center>3</center></td><td><center>509</center></td><td><center>DBA/2J</center></td><td><center>M</center></td><td><center>251197817966</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35918</center></td><td><center>C57BL/6J F B3</center></td><td><center>3</center></td><td><center>5</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197817967</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35919</center></td><td><center>DBA/2J F B3</center></td><td><center>3</center></td><td><center>1</center></td><td><center>DBA/2J</center></td><td><center>F</center></td><td><center>251197817968</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35920</center></td><td><center>C57BL/6J F B3(605)</center></td><td><center>3</center></td><td><center>605</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197817969</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35921</center></td><td><center>B6D2F1 F B3</center></td><td><center>3</center></td><td><center>602</center></td><td><center>B6D2F1</center></td><td><center>F</center></td><td><center>251197817970</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35922</center></td><td><center>B6D2F1 M B3</center></td><td><center>3</center></td><td><center>702</center></td><td><center>B6D2F1</center></td><td><center>M</center></td><td><center>251197817971</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35923</center></td><td><center>BXD14 M</center></td><td><center>3</center></td><td><center>17</center></td><td><center>BXD14</center></td><td><center>M</center></td><td><center>251197817972</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35924</center></td><td><center>BXD15 F</center></td><td><center>3</center></td><td><center>19</center></td><td><center>BXD15</center></td><td><center>F</center></td><td><center>251197817973</center></td></tr> + +<!--Probable error of sex. Should be a male sample based on records, but gene expression suggest that these are females samples--> +<tr bgcolor="#eeeeee"><td><center>35933</center></td><td><center>BXD33 M</center></td><td><center>3</center></td><td><center>39</center></td><td><center>BXD33</center></td><td><center>F or M</center></td><td><center>251197818091</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35925</center></td><td><center>BXD9 F</center></td><td><center>3</center></td><td><center>70</center></td><td><center>BXD9</center></td><td><center>F</center></td><td><center>16011978011756</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35926</center></td><td><center>BXD38 F</center></td><td><center>3</center></td><td><center>52</center></td><td><center>BXD38</center></td><td><center>F</center></td><td><center>16011978011757</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35927</center></td><td><center>BXD36 M</center></td><td><center>3</center></td><td><center>46</center></td><td><center>BXD36</center></td><td><center>M</center></td><td><center>16011978011758</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35928</center></td><td><center>BXD6 M</center></td><td><center>3</center></td><td><center>69</center></td><td><center>BXD6</center></td><td><center>M</center></td><td><center>16011978011759</center></td></tr> + +<!--Probable error of sex. Should be a female sample based on records, but gene expression suggest that these are males samples--> +<tr bgcolor="#eeeeee"><td><center>35929</center></td><td><center>BXDA23F14 F</center></td><td><center>3</center></td><td><center>73</center></td><td><center>BXD86</center></td><td><center>F or M</center></td><td><center>16011978011760</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35930</center></td><td><center>BXDAP5F21 M</center></td><td><center>3</center></td><td><center>86</center></td><td><center>BXD60</center></td><td><center>M</center></td><td><center>16011978011860</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35931</center></td><td><center>BXDAP6F16 F</center></td><td><center>3</center></td><td><center>87</center></td><td><center>BXD44</center></td><td><center>F</center></td><td><center>16011978011861</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35549</center></td><td><center>C57BL/6J F B5</center></td><td><center>5</center></td><td><center>5</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197817949</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35587</center></td><td><center>C57BL/6J F B5R</center></td><td><center>5</center></td><td><center>5</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197818022</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35550</center></td><td><center>DBA/2J F B5</center></td><td><center>5</center></td><td><center>1</center></td><td><center>DBA/2J</center></td><td><center>F</center></td><td><center>251197817950</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35558</center></td><td><center>BXD1 F</center></td><td><center>5</center></td><td><center>11</center></td><td><center>BXD1</center></td><td><center>F</center></td><td><center>251197818036</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35551</center></td><td><center>BXD12 M</center></td><td><center>5</center></td><td><center>14</center></td><td><center>BXD12</center></td><td><center>M</center></td><td><center>251197817952</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35552</center></td><td><center>BXD13 M</center></td><td><center>5</center></td><td><center>15</center></td><td><center>BXD13</center></td><td><center>M</center></td><td><center>251197817953</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35584</center></td><td><center>BXD15 M</center></td><td><center>5</center></td><td><center>18</center></td><td><center>BXD15</center></td><td><center>M</center></td><td><center>251197818034</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35557</center></td><td><center>BXD28 F</center></td><td><center>5</center></td><td><center>28</center></td><td><center>BXD28</center></td><td><center>F</center></td><td><center>251197818035</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35585</center></td><td><center>BXDA10 F</center></td><td><center>5</center></td><td><center>499</center></td><td><center>BXD77</center></td><td><center>F</center></td><td><center>251197818037</center></td></tr> + +<!--Probable error of sex. Should be a male sample based on records, but gene expression suggest that these are females samples--> +<tr bgcolor="#eeeeee"><td><center>35586</center></td><td><center>BXDAP11 M</center></td><td><center>5</center></td><td><center>76</center></td><td><center>BXD51</center></td><td><center>M or F</center></td><td><center>251197818038</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35553</center></td><td><center>BXDAP5 F</center></td><td><center>5</center></td><td><center>84</center></td><td><center>BXD60</center></td><td><center>F</center></td><td><center>251197818019</center></td></tr> + + +<!--RWW: Changed sex of sample 35554 from M to F after genotyping and confirming array data 'sex' --> +<tr bgcolor="#eeeeee"><td><center>35554</center></td><td><center>BXDA22 M</center></td><td><center>5</center></td><td><center>513</center></td><td><center>BXD85</center></td><td><center>F</center></td><td><center>251197818020</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35555</center></td><td><center>BXDAP12 F</center></td><td><center>5</center></td><td><center>515</center></td><td><center>BXD45</center></td><td><center>F</center></td><td><center>251197818021</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35786</center></td><td><center>C57BL/6J F B6</center></td><td><center>6</center></td><td><center>5</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197818004</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35800</center></td><td><center>C57BL/6J F B6R</center></td><td><center>6</center></td><td><center>5</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197818005</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35787</center></td><td><center>DBA/2J F B6</center></td><td><center>6</center></td><td><center>1</center></td><td><center>DBA/2J</center></td><td><center>F</center></td><td><center>251197818006</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35788</center></td><td><center>C57BL/6J M B6(507)</center></td><td><center>6</center></td><td><center>507</center></td><td><center>C57BL/6J</center></td><td><center>M</center></td><td><center>251197818007</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35789</center></td><td><center>DBA/2J M B6(510)</center></td><td><center>6</center></td><td><center>510</center></td><td><center>DBA/2J</center></td><td><center>M</center></td><td><center>251197818008</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35790</center></td><td><center>BXD34 M</center></td><td><center>6</center></td><td><center>42</center></td><td><center>BXD34</center></td><td><center>M</center></td><td><center>251197818114</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35795</center></td><td><center>BXD21 F</center></td><td><center>6</center></td><td><center>20</center></td><td><center>BXD21</center></td><td><center>F</center></td><td><center>251197818115</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35791</center></td><td><center>BXD24 M</center></td><td><center>6</center></td><td><center>26</center></td><td><center>BXD24</center></td><td><center>M</center></td><td><center>251197818116</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35792</center></td><td><center>BXD33 F</center></td><td><center>6</center></td><td><center>40</center></td><td><center>BXD33</center></td><td><center>F</center></td><td><center>251197818117</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35793</center></td><td><center>BXD9 M</center></td><td><center>6</center></td><td><center>71</center></td><td><center>BXD9</center></td><td><center>M</center></td><td><center>251197818118</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35794</center></td><td><center>BXD31 F</center></td><td><center>6</center></td><td><center>32</center></td><td><center>BXD31</center></td><td><center>F</center></td><td><center>251197818119</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35796</center></td><td><center>BXD2 F</center></td><td><center>6</center></td><td><center>612</center></td><td><center>BXD2</center></td><td><center>F</center></td><td><center>251197818120</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35797</center></td><td><center>BXDAP6F16 M</center></td><td><center>6</center></td><td><center>502</center></td><td><center>BXD44</center></td><td><center>M</center></td><td><center>251197818121</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35798</center></td><td><center>BXDAP8F21 M</center></td><td><center>6</center></td><td><center>512</center></td><td><center>BXD48</center></td><td><center>M</center></td><td><center>251197818122</center></td></tr> + +<!--Probable error of sex. Should be a male sample based on records, but gene expression suggest that these are females samples--> +<tr bgcolor="#eeeeee"><td><center>35799</center></td><td><center>BXDA22F14 M</center></td><td><center>6</center></td><td><center>514</center></td><td><center>BXD85</center></td><td><center>M or F</center></td><td><center>251197818123</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35566</center></td><td><center>C57BL/6J F B7</center></td><td><center>7</center></td><td><center>5</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197818023</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35577</center></td><td><center>C57BL/6J F B7R</center></td><td><center>7</center></td><td><center>5</center></td><td><center>C57BL/6J</center></td><td><center>F</center></td><td><center>251197818156</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35567</center></td><td><center>DBA/2J F B7</center></td><td><center>7</center></td><td><center>1</center></td><td><center>DBA/2J</center></td><td><center>F</center></td><td><center>251197818069</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35575</center></td><td><center>DBA/2J M B7</center></td><td><center>7</center></td><td><center>511</center></td><td><center>DBA/2J</center></td><td><center>M</center></td><td><center>251197818070</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35568</center></td><td><center>BXD29 M</center></td><td><center>7</center></td><td><center>31</center></td><td><center>BXD29</center></td><td><center>M</center></td><td><center>251197818071</center></td></tr> + +<!--Probable error of sex. Should be a female sample based on records, but gene expression suggest that these are males samples--> +<tr bgcolor="#eeeeee"><td><center>35569</center></td><td><center>BXD36 F</center></td><td><center>7</center></td><td><center>47</center></td><td><center>BXD36</center></td><td><center>F or M</center></td><td><center>251197818072</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35570</center></td><td><center>BXD38 M</center></td><td><center>7</center></td><td><center>51</center></td><td><center>BXD38</center></td><td><center>M</center></td><td><center>251197818073</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35571</center></td><td><center>BXD39 F</center></td><td><center>7</center></td><td><center>56</center></td><td><center>BXD39</center></td><td><center>F</center></td><td><center>251197818124</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35572</center></td><td><center>BXD40 M</center></td><td><center>7</center></td><td><center>60</center></td><td><center>BXD40</center></td><td><center>M</center></td><td><center>251197818125</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35573</center></td><td><center>BXD42 F</center></td><td><center>7</center></td><td><center>62</center></td><td><center>BXD42</center></td><td><center>F</center></td><td><center>251197818126</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35574</center></td><td><center>BXD5 M</center></td><td><center>7</center></td><td><center>66</center></td><td><center>BXD5</center></td><td><center>M</center></td><td><center>251197818127</center></td></tr> +<tr bgcolor="#eeeeee"><td><center>35579</center></td><td><center>BXD6 F</center></td><td><center>7</center></td><td><center>68</center></td><td><center>BXD6</center></td><td><center>F</center></td><td><center>251197818128</center></td></tr> + +<!--Probable error of sex. Should be a female sample based on records, but gene expression suggest that these are males samples--> +<tr bgcolor="#eeeeee"><td><center>35576</center></td><td><center>BXDAP15 F</center></td><td><center>7</center></td><td><center>78</center></td><td><center>BXD62</center></td><td><center>F or M</center></td><td><center>251197818155</center></td></tr> + + +<tr bgcolor="#eeeeee"><td><center>35508</center></td><td><center>BXDAP19 M</center></td><td><center>7</center></td><td><center>82</center></td><td><center>BXD43</center></td><td><center>M</center></td><td><center>251197818157</center></td></tr> + </table> + </center></td> + </tr> + </table> + </Blockquote> + +<Blockquote> +<P><B>Error Checking Note</B>: Sexes of all individual animals used in this analysis were rechecked by Jing Gu and Lu Lu after processing was complete by genotyping Y chromosome-specific microsatellite markers. <I>Sample 7</I> (also known as <I>Experiment ID 35538</I>) was shown to consist of a pool of two female samples and one male sample. This is the only mixed-sex sample in this study. Sample 513 is a female based both on regenotyping and on the array results. To use the array data to sex an animal we have relied on sex-specific expression differences of gene transcripts. <I>Ddx3y</I> and <I>Uty</I> are good male Y chromosome expression markers, whereas <I>AI314753</I> and <I>Eif2s3x</I> are good female expression markers. Samples 39, 76, and 514 are males based laboratory records and based on regenotyping the Y chromosome, but appear to be females based on the "sex" of the array data. Conversely, sample 47, 73, and 78 should be females based on our records and regenotyping, but appear to be males based on array data. We have marked these uncertain cases as M or F in the table.</P> +</Blockquote> + + +<P class="subtitle"> About data processing:</P> +<Blockquote>Expression data were initially expressed as the ratio of the liver fluorescence signal to that generated by the reference mRNA sample (liver, kidney, lung, brain, and spleen) for each probe. Data were processed using the Agilent version 6.1 <A HREF="http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547" target="_blank" class="normal">feature extractor</A> software. We then computed the log base 2 of these ratios (median). A value of -1 indicates that expression in liver is roughly 1/2 that in the control; a value of -2 indicates that expression in the liver is roughly 1/4 that in the control, etc. Conversely, a value of +2 indicates that the expression in liver 4-fold greater in liver. +</Blockquote> + +<!-- Download the entire original data <a href="./dbdoc/Liver_95_AgilentFea.xls" class="normal">file</a> --> + + +<P class="subtitle"> About the chromosome and megabase position values:</P> + <Blockquote>The chromosomal locations of probes were determined by <A target="_blank" href="http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Tabular&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&NCBI_GI=on&PAGE=MegaBlast&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS.y=8&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes&PERC_IDENT=None,1,-2" class="normal">NCBI's megablast</A> using the NCBIM32 genomic sequence. Gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium May 2004 Assembly (see <A href="http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse" target="_blank" class="normal">http://genome.ucsc.edu/</A> ). We thank Kenneth Phillips (Paradigm Genetics, Inc) for helping in generating probes position data. + </Blockquote> + + +<P class="subtitle"> Data source acknowledgment:</P> +<Blockquote>This project was supported by ES10126, ES11391, ES11660 and P20-MH 62009 to KFM and RW. Ivan Rusyn was a recipient of a Transition to Independent Position Award (ES11660) from the National Institute of Environmental Health Sciences. </blockquote> +<Blockquote>Please contact either:</Blockquote> +<Blockquote><A HREF="http://www.sph.unc.edu/search/profile.cfm?id=2510" target="_blank" class="normal">Ivan Rusyn</A> at the Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431, USA or </Blockquote> +<Blockquote><A target="_blank" HREF="http://www.nervenet.org/people/rob_cv.html" class="normal">Rob Williams</A> at the Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, TN 38163, USA </Blockquote> +</Blockquote> + +<P class="subtitle"> About this text file:</P> + +<Blockquote> +This text file originally generated by Ivan Rusyn, David W. Threadgill and Robert W. Williams, July 2004. Updated by RWW, Nov 14, 16, 2004; by IR, Dec 1, 2004. + +</Blockquote> + +<P></P> + + </center></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--> + + + + </center></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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