aboutsummaryrefslogtreecommitdiff
path: root/web/dbdoc/UAB_DrosWB_LE_RMA_1009.html
diff options
context:
space:
mode:
authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/dbdoc/UAB_DrosWB_LE_RMA_1009.html
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/dbdoc/UAB_DrosWB_LE_RMA_1009.html')
-rwxr-xr-xweb/dbdoc/UAB_DrosWB_LE_RMA_1009.html132
1 files changed, 132 insertions, 0 deletions
diff --git a/web/dbdoc/UAB_DrosWB_LE_RMA_1009.html b/web/dbdoc/UAB_DrosWB_LE_RMA_1009.html
new file mode 100755
index 00000000..095783f7
--- /dev/null
+++ b/web/dbdoc/UAB_DrosWB_LE_RMA_1009.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML><HEAD><TITLE>UAB Whole body D.m. mRNA Lead exposed (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 exposed (Oct09) RMA (accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=250">GN250</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>