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| author | root | 2012-05-08 18:39:56 -0500 |
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| committer | root | 2012-05-08 18:39:56 -0500 |
| commit | ea46f42ee640928b92947bfb204c41a482d80937 (patch) | |
| tree | 9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/dbdoc/UAB_DrosWB_LC_RMA_1009.html | |
| parent | 056b5253fc3857b0444382aa39944f6344dc1ceb (diff) | |
| download | genenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz | |
Add all the source codes into the github.
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diff --git a/web/dbdoc/UAB_DrosWB_LC_RMA_1009.html b/web/dbdoc/UAB_DrosWB_LC_RMA_1009.html new file mode 100755 index 00000000..5be4e8dd --- /dev/null +++ b/web/dbdoc/UAB_DrosWB_LC_RMA_1009.html @@ -0,0 +1,133 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>UAB Whole body D.m. mRNA Lead control (Oct09) 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'> +<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" /> +<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> + +<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT> + +<script src="/javascript/tabbed_pages.js" type="text/javascript"></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> + + <!-- split from Here --> + <!-- Body Start from Here --> + <P class="title">UAB Whole body D.m. mRNA Lead control (Oct09) RMA (accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=249">GN249</A>) <A HREF="/webqtl/main.py?FormID=editHtml"> + <img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> + +<blockquote> +<p class="subtitle">Summary:</p> +<p>The genetics of gene expression in recombinant inbred lines (RILs) can be mapped as expression +quantitative trait loci (eQTLs). So-called ‘‘genetical genomics’’ studies have identified locally acting +eQTLs (cis-eQTLs) for genes that show differences in steady-state RNA levels. These studies have also +identified distantly acting master-modulatory trans-eQTLs that regulate tens or hundreds of transcripts +(hotspots or transbands). We expand on these studies by performing genetical genomics experiments in +two environments in order to identify trans-eQTL thatmight be regulated by developmental exposure to +the neurotoxin lead. Flies from each of 75 RIL were raised from eggs to adults on either control food +(made with 250 mM sodium acetate), or lead-treated food (made with 250 mM lead acetate, PbAc). RNA +expression analyses of whole adult male flies (5–10 days old) were performed with Affymetrix DrosII +whole genome arrays (18,952 probesets). Among the 1389 genes with cis-eQTL, there were 405 genes +unique to control flies and 544 genes unique to lead-treated ones (440 genes had the same cis-eQTLs in +both samples). There are 2396 genes with trans-eQTL which mapped to 12major transbands with greater +than 95 genes. Permutation analyses of the strain labels but not the expression data suggests that the +total number of eQTL and the number of transbands are more important criteria for validation than the +size of the transband. Two transbands, one located on the 2nd chromosome and one on the 3rd +chromosome, co-regulate 33 lead-induced genes, many of which are involved in neurodevelopmental +processes. For these 33 genes, rather than allelic variation at one locus exerting differential effects in two +environments, we found that variation at two different loci are required for optimal effects on leadinduced +expression.</p> +<p class="subtitle">Materials and Methods:</p> +<p>The 75 Drosophila roo lines were obtained from Trudy Mackay. +To avoid batch effects (Zakharkin et al., 2005), the growth of the +flies, the RNA extraction and the order of running the arrays, and +the fluidics well used for each array was completely randomized +for the 75 lines in two treatments. Control food consisted of +standard cornmeal, agar, sugar, yeast, and 250 mM NaAc (Ashburner, +1989). Lead-contaminated food consisted of standard food +plus 250 mM PbAc (lead exposure at this concentration has been +shown to affect locomotion in adults; Hirsch et al., 2003). Flies +from each of the 75 roo lines (20 males and 20 females) were +placed in a vial with 10 ml of food (control or PbAc) for 3 days at +25 8C and allowed to lay eggs; the adults were subsequently +discarded. Newly enclosed adult males were placed on the same +medium (control or PbAc) as had been present during pre-adult +development for 5–10 days before being used as subjects. Male +progeny were pooled from each vial (65 males per vial) and frozen +at 80 8C. RNA samples were extracted in groups of 24 and arrays +hybridization run in groups of 4 with 3 groups run per day. Effects +of RNA extraction and array hybridizations day were examined by +ANOVA and Support Vector approaches and no obvious day effects +were observed.</p> +<p class="subtitle">Data Source Acknowledgements:</p> +<p> +<p>This work was supported by the Environmental Health Sciences +Center in Molecular and Cellular Toxicology with Human +Applications Grant P30 ES06639 at Wayne State University, NIH +R01 grants ES012933 and CA105349 to D.M.R., DK071073 to X.L., +and UAB-CNGI grant to M.D.G. We thank H. Ghiradella for critical +comments on the manuscript. The microarray data is freely +available to the public, in the MIAME format in 150 CEL files, in the +GEO database under GSE 11695.<p>Please cite this article in press as: Ruden DM, et al. Genetical toxicogenomics in Drosophila identifies master-modulatory loci that are +regulated by developmental exposure to lead, Neurotoxicology (2009), doi:10.1016/j.neuro.2009.08.011<p><a href="http://www.genenetwork.org/dbdoc/Neurotox_2009_eQTL.pdf">Full Article</a></p> +</blockquote> + + </TR></TABLE> + </TD> + </TR> + <TR> + <TD align=center bgColor=#ddddff class="solidBorder"> + <!--Start of footer--> + <TABLE width="90%"> + <script language='JavaScript' src='/javascript/footer.js'></script> + <TR> + <TD colspan=3 class="fs12"> + <UL> + + </UL> + </TD> + </TR> + </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. Always put it before </body> + // each menu gets two parameters (see demo files) + // 1. items structure + // 2. geometry structure + new menu (MENU_ITEMS, MENU_POS); + // make sure files containing definitions for these variables are linked to the document + // if you got some javascript error like "MENU_POS is not defined", then you've made syntax + // error in menu_tpl.js file or that file isn't linked properly. + + // also take a look at stylesheets loaded in header in order to set styles + //--> + +</script> +</BODY> +</HTML> |