1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD><TITLE>MDC/CAS/UCL Heart 230_V2 (Dec08) 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>
<SCRIPT SRC="/javascript/dhtml.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>
<!-- split from Here -->
<!-- Body Start from Here -->
<P class="title">MDC/CAS/UCL Heart 230_V2 (Dec08) 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=221">GN221</A></P>
<Blockquote>
<P>Heart Left Ventricle
<P>http://www.expressionanalysis.com/pdf/Affymetrix/GXRat230v2.pdf
<P>GEO platform id http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL1355
<P>Data entered by Evan Williams and Rob Williams, Jan 2, 2009.
<P>Mapping of probes http://compbio.dcs.gla.ac.uk/sf/index.html#230map
<P>Entered by Arthur Centeno, Dec 18, 2008. Data from Herbert Schulz. CEL files processed by AC. Data normalized by AC and RWW (2z+8).
<P>Access to this data set is currently limited to the three teams of researchers who generated the data: Norbert Hübner (MDC, Berlin), Timothy Aitman (UC London), and Michal Pravenec (CAS, Prague). For access to data please contact N. Hübner by email.
<P>The text below was copied from the INFO file for the older (2005) kidney gene expression data set by RWW (Dec 20, 2008). It contains errors and will need to be corrected with the guidance of the data generators and owners.
</Blockquote>
<P class="subtitle">Summary:</P>
<Blockquote><P>
This December 2008 data set provides estimates of mRNA expression in normal hearts of 31 strains of rats including the hypertensive SHR strain (aka HSR), the normotensive BN strain, and 29 HXB/BXH recombinant inbred strains. Most strains were sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center (MDC), Berlin Buch by <A HREF="http://www.mdc-berlin.de/en/phd_ausbildung/phd_program/TransCard_Research_School/Prospective_Students/Faculty/Genetic_Susceptibility/Norbert_H__bner/index.html" target="_blank" class="fs14">Norbert Hübner</A> and colleagues. Transcriptome mapping was carried out by Timothy Aitman and colleagues at the Imperial College, London (ICL). Samples were hybridized individually to a total of approximately XXX Affymetrix RAE230A array processed using the RMA protocol. The expression values of each array have been logged and adjusted to a mean of 8 and a standard deviation of 2 (mean and variance stabilized). This data set complements the kidney and fat data set exploited by Hübner and colleagues <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15711544" target="_blank" class="fs14">2005</A>.
</P>
<P>These data may also be viewed using the <A HREF="http://web.bioinformatics.ic.ac.uk/eqtlexplorer/" target="_blank" class="fs14">eQTL Explorer</A> Java application
by John Mangion, Tim Aitman, and colleagues (Mueller et al. <A HREF="http://bioinformatics.oxfordjournals.org/cgi/reprint/btk007v1.pdf
" target="_blank" class="fs14">2006</A>).
</Blockquote>
<P class="subtitle">About the cases used to generate this set of data:</P>
<Blockquote>Data were generated using the HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv, abbreviated SHR or HSR = H) and Brown Norway (BN-Lx/Cub= B). These strains have been used extensively to study cardiovascular system physiology and genetics.</P>
<P>The HXB strains were bred by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were bred by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 6oth generation of continuous inbreeding (F60).</P>
<P>Animals used in the transcriptome analyses of multiple tissues (Hübner and colleagues, <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15711544" target="_blank" class="fs14">2005</A>) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commerical rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 deg. C. Rats were sexually naive. All males used in the initial transcriptome studies (Hübner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protectiion Law of the Czech Republic (311/1997).
</Blockquote>
<P class="subtitle">About the tissue used to generate these data:</P>
<Blockquote>All tissues were collected at the age of 6 weeks. Hearts and other organs were rapidly dissected and cleaned of fat, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction.
THIS IS AN OLD TABLE FOR THE KIDNEY DATA IN THIS INFO FILE ONLY AS A PLACEHOLDER. The table below lists the arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat.
</Blockquote>
<table border="0" cellpadding="0" cellspacing="0" bgcolor="#000000" width="50%" align="Center">
<tr>
<td>
<table width="100%" border="0" cellpadding="5" cellspacing="1">
<tr bgcolor="royalblue">
<td><font color=#FFFFFF>Strain</font></td>
<td><font color=#FFFFFF>SampleID</font></td>
</tr>
<tr bgcolor="#eeeeee"><td>HSR</td><td>HSR1</td>
<tr bgcolor="#eeeeee"><td>HSR</td><td>HSR2</td>
<tr bgcolor="#eeeeee"><td>HSR</td><td>HSR3</td>
<tr bgcolor="#eeeeee"><td>HSR</td><td>HSR4</td>
<tr bgcolor="#eeeeee"><td>BN</td><td>BN1</td>
<tr bgcolor="#eeeeee"><td>BN</td><td>BN2</td>
<tr bgcolor="#eeeeee"><td>BN</td><td>BN3</td>
<tr bgcolor="#eeeeee"><td>BN</td><td>BN4</td>
<tr bgcolor="#eeeeee"><td>BN</td><td>BN5</td>
<tr bgcolor="#eeeeee"><td>HXB1</td><td>RI 01-1</td>
<tr bgcolor="#eeeeee"><td>HXB1</td><td>RI 01-2</td>
<tr bgcolor="#eeeeee"><td>HXB1</td><td>RI 01-3</td>
<tr bgcolor="#eeeeee"><td>HXB1</td><td>RI 01-4</td>
<tr bgcolor="#eeeeee"><td>HXB2</td><td>RI 02-1</td>
<tr bgcolor="#eeeeee"><td>HXB2</td><td>RI 02-2</td>
<tr bgcolor="#eeeeee"><td>HXB2</td><td>RI 02-3</td>
<tr bgcolor="#eeeeee"><td>HXB2</td><td>RI 02-4</td>
<tr bgcolor="#eeeeee"><td>HXB3</td><td>RI 03-1</td>
<tr bgcolor="#eeeeee"><td>HXB3</td><td>RI 03-2</td>
<tr bgcolor="#eeeeee"><td>HXB3</td><td>RI 03-3</td>
<tr bgcolor="#eeeeee"><td>HXB3</td><td>RI 03-4</td>
<tr bgcolor="#eeeeee"><td>HXB4</td><td>RI 04-1</td>
<tr bgcolor="#eeeeee"><td>HXB4</td><td>RI 04-2</td>
<tr bgcolor="#eeeeee"><td>HXB4</td><td>RI 04-3</td>
<tr bgcolor="#eeeeee"><td>HXB4</td><td>RI 04-4</td>
<tr bgcolor="#eeeeee"><td>HXB5</td><td>RI 05-1</td>
<tr bgcolor="#eeeeee"><td>HXB5</td><td>RI 05-2</td>
<tr bgcolor="#eeeeee"><td>HXB5</td><td>RI 05-3</td>
<tr bgcolor="#eeeeee"><td>HXB5</td><td>*RI 05-4</td>
<tr bgcolor="#eeeeee"><td>HXB7</td><td>RI 07-1</td>
<tr bgcolor="#eeeeee"><td>HXB7</td><td>RI 07-2</td>
<tr bgcolor="#eeeeee"><td>HXB7</td><td>RI 07-3</td>
<tr bgcolor="#eeeeee"><td>HXB7</td><td>RI 07-4</td>
<tr bgcolor="#eeeeee"><td>HXB10</td><td>RI 10-1</td>
<tr bgcolor="#eeeeee"><td>HXB10</td><td>RI 10-2</td>
<tr bgcolor="#eeeeee"><td>HXB10</td><td>RI 10-3</td>
<tr bgcolor="#eeeeee"><td>HXB10</td><td>RI 10-4</td>
<tr bgcolor="#eeeeee"><td>HXB15</td><td>RI 15-1</td>
<tr bgcolor="#eeeeee"><td>HXB15</td><td>RI 15-2</td>
<tr bgcolor="#eeeeee"><td>HXB15</td><td>RI 15-3</td>
<tr bgcolor="#eeeeee"><td>HXB15</td><td>RI 15-4</td>
<tr bgcolor="#eeeeee"><td>HXB17</td><td>RI 17-1</td>
<tr bgcolor="#eeeeee"><td>HXB17</td><td>RI 17-2</td>
<tr bgcolor="#eeeeee"><td>HXB17</td><td>RI 17-3</td>
<tr bgcolor="#eeeeee"><td>HXB17</td><td>RI 17-4</td>
<tr bgcolor="#eeeeee"><td>HXB18</td><td>RI 18-1</td>
<tr bgcolor="#eeeeee"><td>HXB18</td><td>RI 18-2</td>
<tr bgcolor="#eeeeee"><td>HXB18</td><td>RI 18-3</td>
<tr bgcolor="#eeeeee"><td>HXB18</td><td>RI 18-4</td>
<tr bgcolor="#eeeeee"><td>HXB20</td><td>RI 20-1</td>
<tr bgcolor="#eeeeee"><td>HXB20</td><td>RI 20-2</td>
<tr bgcolor="#eeeeee"><td>HXB20</td><td>RI 20-3</td>
<tr bgcolor="#eeeeee"><td>HXB20</td><td>RI 20-4</td>
<tr bgcolor="#eeeeee"><td>HXB21</td><td>RI 21-1</td>
<tr bgcolor="#eeeeee"><td>HXB21</td><td>RI 21-2</td>
<tr bgcolor="#eeeeee"><td>HXB21</td><td>RI 21-3</td>
<tr bgcolor="#eeeeee"><td>HXB21</td><td>RI 21-4</td>
<tr bgcolor="#eeeeee"><td>HXB22</td><td>RI 22-1</td>
<tr bgcolor="#eeeeee"><td>HXB22</td><td>RI 22-2</td>
<tr bgcolor="#eeeeee"><td>HXB22</td><td>RI 22-3</td>
<tr bgcolor="#eeeeee"><td>HXB22</td><td>RI 22-4</td>
<tr bgcolor="#eeeeee"><td>HXB23</td><td>RI 23-1</td>
<tr bgcolor="#eeeeee"><td>HXB23</td><td>RI 23-2</td>
<tr bgcolor="#eeeeee"><td>HXB23</td><td>RI 23-3</td>
<tr bgcolor="#eeeeee"><td>HXB23</td><td>RI 23-4</td>
<tr bgcolor="#eeeeee"><td>HXB24</td><td>RI 24-1</td>
<tr bgcolor="#eeeeee"><td>HXB24</td><td>RI 24-2</td>
<tr bgcolor="#eeeeee"><td>HXB24</td><td>RI 24-3</td>
<tr bgcolor="#eeeeee"><td>HXB24</td><td>RI 24-4</td>
<tr bgcolor="#eeeeee"><td>HXB25</td><td>RI 25-1</td>
<tr bgcolor="#eeeeee"><td>HXB25</td><td>RI 25-2</td>
<tr bgcolor="#eeeeee"><td>HXB25</td><td>RI 25-3</td>
<tr bgcolor="#eeeeee"><td>HXB25</td><td>*RI 25-4</td>
<tr bgcolor="#eeeeee"><td>HXB26</td><td>RI 26-1</td>
<tr bgcolor="#eeeeee"><td>HXB26</td><td>RI 26-2</td>
<tr bgcolor="#eeeeee"><td>HXB26</td><td>RI 26-3</td>
<tr bgcolor="#eeeeee"><td>HXB26</td><td>RI 26-4</td>
<tr bgcolor="#eeeeee"><td>HXB27</td><td>RI 27-1</td>
<tr bgcolor="#eeeeee"><td>HXB27</td><td>RI 27-2</td>
<tr bgcolor="#eeeeee"><td>HXB27</td><td>RI 27-3</td>
<tr bgcolor="#eeeeee"><td>HXB27</td><td>RI 27-4</td>
<tr bgcolor="#eeeeee"><td>HXB29</td><td>RI 29-1</td>
<tr bgcolor="#eeeeee"><td>HXB29</td><td>RI 29-2</td>
<tr bgcolor="#eeeeee"><td>HXB29</td><td>RI 29-3</td>
<tr bgcolor="#eeeeee"><td>HXB29</td><td>RI 29-4</td>
<tr bgcolor="#eeeeee"><td>HXB31</td><td>RI 31-1</td>
<tr bgcolor="#eeeeee"><td>HXB31</td><td>RI 31-2</td>
<tr bgcolor="#eeeeee"><td>HXB31</td><td>RI 31-3</td>
<tr bgcolor="#eeeeee"><td>HXB31</td><td>RI 31-4</td>
<tr bgcolor="#eeeeee"><td>BXH2</td><td>RI 02c-1</td>
<tr bgcolor="#eeeeee"><td>BXH2</td><td>RI 02c-2</td>
<tr bgcolor="#eeeeee"><td>BXH2</td><td>RI 02c-3</td>
<tr bgcolor="#eeeeee"><td>BXH2</td><td>RI 02c-4</td>
<tr bgcolor="#eeeeee"><td>BXH3</td><td>RI 03c-1</td>
<tr bgcolor="#eeeeee"><td>BXH3</td><td>RI 03c-2</td>
<tr bgcolor="#eeeeee"><td>BXH3</td><td>RI 03c-3</td>
<tr bgcolor="#eeeeee"><td>BXH3</td><td>RI 03c-4</td>
<tr bgcolor="#eeeeee"><td>BXH5</td><td>RI 05c-1</td>
<tr bgcolor="#eeeeee"><td>BXH5</td><td>RI 05c-2</td>
<tr bgcolor="#eeeeee"><td>BXH5</td><td>RI 05c-3</td>
<tr bgcolor="#eeeeee"><td>BXH5</td><td>RI 05c-4</td>
<tr bgcolor="#eeeeee"><td>BXH6</td><td>RI 06c-1</td>
<tr bgcolor="#eeeeee"><td>BXH6</td><td>RI 06c-2</td>
<tr bgcolor="#eeeeee"><td>BXH6</td><td>RI 06c-3</td>
<tr bgcolor="#eeeeee"><td>BXH6</td><td>RI 06c-4</td>
<tr bgcolor="#eeeeee"><td>BXH8</td><td>RI 08c-1</td>
<tr bgcolor="#eeeeee"><td>BXH8</td><td>RI 08c-2</td>
<tr bgcolor="#eeeeee"><td>BXH8</td><td>RI 08c-3</td>
<tr bgcolor="#eeeeee"><td>BXH8</td><td>RI 08c-4</td>
<tr bgcolor="#eeeeee"><td>BXH9</td><td>RI 09c-1</td>
<tr bgcolor="#eeeeee"><td>BXH9</td><td>RI 09c-2</td>
<tr bgcolor="#eeeeee"><td>BXH9</td><td>RI 09c-3</td>
<tr bgcolor="#eeeeee"><td>BXH9</td><td>RI 09c-4</td>
<tr bgcolor="#eeeeee"><td>BXH10</td><td>RI 10c-1</td>
<tr bgcolor="#eeeeee"><td>BXH10</td><td>RI 10c-2</td>
<tr bgcolor="#eeeeee"><td>BXH10</td><td>RI 10c-3</td>
<tr bgcolor="#eeeeee"><td>BXH11</td><td>RI 11c-1</td>
<tr bgcolor="#eeeeee"><td>BXH11</td><td>RI 11c-2</td>
<tr bgcolor="#eeeeee"><td>BXH11</td><td>RI 11c-3</td>
<tr bgcolor="#eeeeee"><td>BXH11</td><td>RI 11c-4</td>
<tr bgcolor="#eeeeee"><td>BXH12</td><td>RI 12c-1</td>
<tr bgcolor="#eeeeee"><td>BXH12</td><td>RI 12c-2</td>
<tr bgcolor="#eeeeee"><td>BXH12</td><td>RI 12c-3</td>
<tr bgcolor="#eeeeee"><td>BXH12</td><td>RI 12c-4</td>
<tr bgcolor="#eeeeee"><td>BXH13</td><td>RI 13c-1</td>
<tr bgcolor="#eeeeee"><td>BXH13</td><td>RI 13c-2</td>
<tr bgcolor="#eeeeee"><td>BXH13</td><td>RI 13c-3</td>
<tr bgcolor="#eeeeee"><td>BXH13</td><td>RI 13c-4</td>
</table>
</td>
</tr>
</table>
<P class="subtitle">About the array platform:</P>
<Blockquote><P>
<B>Affymetrix 230Av2 GeneChip:</B> Expression data were generated using the Affymetrix 230Av2 array (<a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL341" target="_blank">GEO_GPL341</a>). The chromosomal locations of probe sets were determined by <a href="http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=rat" target="_blank" class="fs14">BLAT</A> analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.</P>
</Blockquote>
<P class="subtitle">Control Procedures:</P>
<Blockquote>
<P><B>RNA processing:</B>RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. The Ambion MEGAscript T7 kit from Ambion was used to generate biotinylated cRNA for kidney. See Hübner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control steps.</P>
</Blockquote>
<P class="subtitle">About data processing:</P>
<Blockquote><B>Probe (cell) level data from the CEL file: </B>These CEL values produced by <a target="_blank" class="fs14" href="http://www.affymetrix.com/support/technical/product_updates/gcos_download.affx">GCOS</a> are 75% quantiles from a set of pixel measured in each cell.
<P><B>Probe set data: </B>The original CEL values were processed using RMA and log2 transformed using our standard 2z +8 transform. This recenters each array to a mean of 8 units and a SD of 2 units. Probe set values are typically the averages of four biological replicates within strain. </P>
</Blockquote>
<P class="subtitle">Data source acknowledgment:</P>
<Blockquote>
This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Initiative; to NH from the German Ministry for Science and Education (National Genome Research Network); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. Michal Pravenec thanks the Howard Hughes Medical Institute for its support to him as an international research scholar.
</Blockquote>
<P class="subtitle">Information about this text file:</P>
<Blockquote><P>This text file originally copied from the old kidney INFO file that was generated by Robert Williams, Norbert Hübner, Michal Pravnec, Timothy Aitman. This version entered into the adrenal INFO file, December 19, 2008, by RWW, Kathrin Saar Dec 23.
</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>
|
