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diff --git a/web/dbdoc/UAB_DrosWB_LC_RMA_1009.html b/web/dbdoc/UAB_DrosWB_LC_RMA_1009.html deleted file mode 100755 index 5be4e8dd..00000000 --- a/web/dbdoc/UAB_DrosWB_LC_RMA_1009.html +++ /dev/null @@ -1,133 +0,0 @@ -<!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. 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