diff options
Diffstat (limited to 'general/datasets/RTC_1106_R')
| -rw-r--r-- | general/datasets/RTC_1106_R/acknowledgment.rtf | 5 | ||||
| -rw-r--r-- | general/datasets/RTC_1106_R/cases.rtf | 914 | ||||
| -rw-r--r-- | general/datasets/RTC_1106_R/experiment-design.rtf | 7 | ||||
| -rw-r--r-- | general/datasets/RTC_1106_R/notes.rtf | 1 | ||||
| -rw-r--r-- | general/datasets/RTC_1106_R/platform.rtf | 3 | ||||
| -rw-r--r-- | general/datasets/RTC_1106_R/processing.rtf | 6 | ||||
| -rw-r--r-- | general/datasets/RTC_1106_R/summary.rtf | 3 |
7 files changed, 939 insertions, 0 deletions
diff --git a/general/datasets/RTC_1106_R/acknowledgment.rtf b/general/datasets/RTC_1106_R/acknowledgment.rtf new file mode 100644 index 0000000..3246da5 --- /dev/null +++ b/general/datasets/RTC_1106_R/acknowledgment.rtf @@ -0,0 +1,5 @@ +<blockquote>
+<p>These data were generated by Prof. Dr. Klaus Schughart (Department of Experimental Mouse Genetics) and Dr. Dunja Bruder (Research Group Immune Regulation) at the Helmholtz Center for Infection Research with the help of Dr. Lothar Gröbe (FACS sorting, Research Group Mucosal Immunity).</p>
+
+<p>Funding was provided by the Helmholtz Association and publicly funded research projects awarded to Drs. Klaus Schughart and Dunja Bruder.</p>
+</blockquote>
diff --git a/general/datasets/RTC_1106_R/cases.rtf b/general/datasets/RTC_1106_R/cases.rtf new file mode 100644 index 0000000..5ae01c7 --- /dev/null +++ b/general/datasets/RTC_1106_R/cases.rtf @@ -0,0 +1,914 @@ +<blockquote>
+<p>Parental and 31 BXD lines were studied. Mice were received from The Jackson Laboratory, or from The Oak Ridge National and were bred in the facility of the Neuro-BSIK consortium (VU University Amsterdam). The data set includes expression values for 18 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD40), as well as the two parental strains, C57BL/6J and DBA/2J. All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding.</p>
+
+<p>BXD spleen sample pools (from 2-3 mice) were obtained from a pathogen-free mice of the Dutch Mouse Phenomics Consortium (MPC) in Amsterdam. Mice were imported into the central animal facility at the HZI and kept in a pathogen-free vivarium. Mice were euthanized using CO2 and spleenocytes were prepared. Most mice were between 17 and 22 weeks of age when samples were collected. FACS sorting was used to select the CD4-positive T cells. These cells were further separated into CD4+CD25+ and CD4+CD25- pools.</p>
+
+<p>Error-checking strain identity. A set of more than 20 probe sets with Mendelian segregation patterns in this HZI data set were used to confirm strain identify in early June, 2007. Two errors were detected and rectified. As of June 22, 2007, data are registered correctly. Prior to June 22, 2007, data listed as strains BXD33 and BXD39 were essentially hybrid (mixed) data sets.</p>
+
+<p>On Aug 23, 2007, we loaded the final QTL Reaper data into GeneNetwork for the corrected data set. The maximum LRS generated by any probe set is 84.6 for 1436240_at (<em>Tra2a</em>). A total of 41 probe sets are associated with QTLs that have LRS values above 46 (LOD > 10).</p>
+
+<p>Sex of samples is listed below in Table 1. In brief, data for BXD14 and 23 are male-only samples, whereas BXD12, 16, 31, 34, 36 and C57BL/6J are from female-only samples. All other samples (DBA/2J, BXD1, 2, 6, 9, 11, 18, 21 32, 33, 39, 40) consist of one male and one female array. The sex of samples can be independently validated using the <em>Xist</em> probe set (1427262_at).</p>
+
+<p><img src="http://www.genenetwork.org/images/upload/HZi_sex.gif" /></p>
+
+<p><small><strong>Figure 1:</strong> The expression of <em>Xist</em> can be used as an independent marker for sex. Xist is expressed at very low levels (noise) in male samples (far left) and at high values in females (far right). Sex-balanced samples (middle) have high variance due to the inclusion of one array per sex. </small></p>
+
+<p> Table 1</p>
+
+<blockquote>
+<table border="1" cellpadding="0" cellspacing="0" style="width:600px">
+ <tbody>
+ <tr>
+ <td>
+ <table align="left" border="1" cellpadding="5" cellspacing="1" style="width:600px">
+ <tbody>
+ <tr>
+ <td>Index</td>
+ <td>ProbeSet ID</td>
+ <td>Sample Description</td>
+ <td>Sex</td>
+ <td>Strain</td>
+ <td>cd25</td>
+ <td>Microarray</td>
+ <td>Short Description</td>
+ <td>Age</td>
+ <td>Pool No.</td>
+ <td>Pool members (animal number)</td>
+ <td>Date of preparation</td>
+ </tr>
+ <tr>
+ <td>1</td>
+ <td>HZI1008</td>
+ <td>BXD-06f (f1) CD25+</td>
+ <td>F</td>
+ <td>BXD6</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-06f</td>
+ <td>17</td>
+ <td>f1</td>
+ <td>1,3,4</td>
+ <td>1-31-2006</td>
+ </tr>
+ <tr>
+ <td>2</td>
+ <td>HZI1009</td>
+ <td>BXD-06m (m2) CD25+</td>
+ <td>M</td>
+ <td>BXD6</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-06m</td>
+ <td>18</td>
+ <td>m2</td>
+ <td>5,6,7</td>
+ <td>1-31-2006</td>
+ </tr>
+ <tr>
+ <td>3</td>
+ <td>HZI1010</td>
+ <td>BXD-14m (m3) CD25+</td>
+ <td>M</td>
+ <td>BXD14</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-14m</td>
+ <td>17</td>
+ <td>m3</td>
+ <td>1,3,4</td>
+ <td>1-31-2006</td>
+ </tr>
+ <tr>
+ <td>4</td>
+ <td>HZI1013</td>
+ <td>BXD-40f (f6) CD25+</td>
+ <td>F</td>
+ <td>BXD40</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-40f</td>
+ <td>17</td>
+ <td>f6</td>
+ <td>1,2,3</td>
+ <td>2-1-2006</td>
+ </tr>
+ <tr>
+ <td>5</td>
+ <td>HZI1014</td>
+ <td>BXD-40m (m7) CD25+</td>
+ <td>M</td>
+ <td>BXD40</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-40m</td>
+ <td>17</td>
+ <td>m7</td>
+ <td>5,6,7</td>
+ <td>2-2-2006</td>
+ </tr>
+ <tr>
+ <td>6</td>
+ <td>HZI1015</td>
+ <td>BXD-02f (f8) CD25+</td>
+ <td>F</td>
+ <td>BXD2</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-02f</td>
+ <td>17</td>
+ <td>f8</td>
+ <td>1,2,3</td>
+ <td>2-14-2006</td>
+ </tr>
+ <tr>
+ <td>7</td>
+ <td>HZI1016</td>
+ <td>BXD-02m (m20) CD25+</td>
+ <td>M</td>
+ <td>BXD2</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-02m</td>
+ <td>21</td>
+ <td>m20</td>
+ <td>4,5,6</td>
+ <td>4-6-2006</td>
+ </tr>
+ <tr>
+ <td>8</td>
+ <td>HZI1017</td>
+ <td>BXD-11f (f30) CD25+</td>
+ <td>F</td>
+ <td>BXD11</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-11f</td>
+ <td>17</td>
+ <td>f30</td>
+ <td>3,4,5</td>
+ <td>5-11-2006</td>
+ </tr>
+ <tr>
+ <td>9</td>
+ <td>HZI1018</td>
+ <td>BXD-11m (m9) CD25+</td>
+ <td>M</td>
+ <td>BXD11</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-11m</td>
+ <td>18</td>
+ <td>m9</td>
+ <td>1,2</td>
+ <td>2-14-2006</td>
+ </tr>
+ <tr>
+ <td>10</td>
+ <td>HZI1019</td>
+ <td>BXD-12f (f10) CD25+</td>
+ <td>F</td>
+ <td>BXD12</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-12f</td>
+ <td>17</td>
+ <td>f10</td>
+ <td>1,2,3</td>
+ <td>2-14-2006</td>
+ </tr>
+ <tr>
+ <td>11</td>
+ <td>HZI1020</td>
+ <td>BXD-39f (f23) CD25+</td>
+ <td>F</td>
+ <td>BXD39</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-39f</td>
+ <td>19</td>
+ <td>f23</td>
+ <td>4,5,6</td>
+ <td>4-11-2006</td>
+ </tr>
+ <tr>
+ <td>12</td>
+ <td>HZI1021</td>
+ <td>BXD-33m (m11) CD25+</td>
+ <td>M</td>
+ <td>BXD33</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-33m</td>
+ <td>17</td>
+ <td>m11</td>
+ <td>1,2</td>
+ <td>2-14-2006</td>
+ </tr>
+ <tr>
+ <td>13</td>
+ <td>HZI1022</td>
+ <td>BXD-18f (f14) CD25+</td>
+ <td>F</td>
+ <td>BXD18</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-18f</td>
+ <td>17</td>
+ <td>f14</td>
+ <td>3,4,5</td>
+ <td>2-15-2006</td>
+ </tr>
+ <tr>
+ <td>14</td>
+ <td>HZI1023</td>
+ <td>BXD-18m (m13) CD25+</td>
+ <td>M</td>
+ <td>BXD18</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-18m</td>
+ <td>18</td>
+ <td>m13</td>
+ <td>7,8</td>
+ <td>2-15-2006</td>
+ </tr>
+ <tr>
+ <td>15</td>
+ <td>HZI1024</td>
+ <td>BXD-23m (m15) CD25+</td>
+ <td>M</td>
+ <td>BXD23</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-23m</td>
+ <td>18</td>
+ <td>m15</td>
+ <td>1,2,3</td>
+ <td>2-15-2006</td>
+ </tr>
+ <tr>
+ <td>16</td>
+ <td>HZI1026</td>
+ <td>BXD-09f (f17) CD25+</td>
+ <td>F</td>
+ <td>BXD9</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-09f</td>
+ <td>21</td>
+ <td>f17</td>
+ <td>1,2,3</td>
+ <td>4-5-2006</td>
+ </tr>
+ <tr>
+ <td>17</td>
+ <td>HZI1028</td>
+ <td>BXD-09m (m35) CD25+</td>
+ <td>M</td>
+ <td>BXD9</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-09m</td>
+ <td>15</td>
+ <td>m35</td>
+ <td>7,8,9</td>
+ <td>7-7-2006</td>
+ </tr>
+ <tr>
+ <td>18</td>
+ <td>HZI1029</td>
+ <td>BXD-32f (f18) CD25+</td>
+ <td>F</td>
+ <td>BXD32</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-32f</td>
+ <td>21</td>
+ <td>f18</td>
+ <td>1,2,3</td>
+ <td>4-6-2006</td>
+ </tr>
+ <tr>
+ <td>19</td>
+ <td>HZI1030</td>
+ <td>BXD-32m (m19) CD25+</td>
+ <td>M</td>
+ <td>BXD32</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-32m</td>
+ <td>22</td>
+ <td>m19</td>
+ <td>1,2,3</td>
+ <td>4-6-2006</td>
+ </tr>
+ <tr>
+ <td>20</td>
+ <td>HZI1031</td>
+ <td>BXD-33f (f22) CD25+</td>
+ <td>F</td>
+ <td>BXD33</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-33f</td>
+ <td>18</td>
+ <td>f22</td>
+ <td>2,3,4</td>
+ <td>4-11-2006</td>
+ </tr>
+ <tr>
+ <td>21</td>
+ <td>HZI1032</td>
+ <td>BXD-39m (m29) CD25+</td>
+ <td>M</td>
+ <td>BXD39</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-39m</td>
+ <td>17</td>
+ <td>m29</td>
+ <td>5,6,7</td>
+ <td>5-10-2006</td>
+ </tr>
+ <tr>
+ <td>22</td>
+ <td>HZI1033</td>
+ <td>BXD-01f (f32) CD25+</td>
+ <td>F</td>
+ <td>BXD1</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-01f</td>
+ <td>18</td>
+ <td>f32</td>
+ <td>3,4</td>
+ <td>7-6-2006</td>
+ </tr>
+ <tr>
+ <td>23</td>
+ <td>HZI1034</td>
+ <td>BXD-01m (m31) CD25+</td>
+ <td>M</td>
+ <td>BXD1</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-01m</td>
+ <td>18</td>
+ <td>m31</td>
+ <td>1,2</td>
+ <td>7-6-2006</td>
+ </tr>
+ <tr>
+ <td>24</td>
+ <td>HZI1035</td>
+ <td>BXD-16f (f26) CD25+</td>
+ <td>F</td>
+ <td>BXD16</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-16f</td>
+ <td>18</td>
+ <td>f26</td>
+ <td>1,2,3</td>
+ <td>4-12-2006</td>
+ </tr>
+ <tr>
+ <td>25</td>
+ <td>HZI1036</td>
+ <td>BXD-21f (f25) CD25+</td>
+ <td>F</td>
+ <td>BXD21</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-21f</td>
+ <td>19</td>
+ <td>f25</td>
+ <td>5,6,7</td>
+ <td>4-12-2006</td>
+ </tr>
+ <tr>
+ <td>26</td>
+ <td>HZI1037</td>
+ <td>BXD-21m (m24) CD25+</td>
+ <td>M</td>
+ <td>BXD21</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-21m</td>
+ <td>18</td>
+ <td>m24</td>
+ <td>1,2,3</td>
+ <td>4-12-2006</td>
+ </tr>
+ <tr>
+ <td>27</td>
+ <td>HZI1039</td>
+ <td>BXD-31f (f34) CD25+</td>
+ <td>F</td>
+ <td>BXD31</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-31f</td>
+ <td>16</td>
+ <td>f34</td>
+ <td>1,2,3</td>
+ <td>7-7-2006</td>
+ </tr>
+ <tr>
+ <td>28</td>
+ <td>HZI1040</td>
+ <td>C57BL/6Jf (f28) CD25+</td>
+ <td>F</td>
+ <td>C57BL/6J</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>C57BL/6Jf</td>
+ <td>16</td>
+ <td>f28</td>
+ <td>1,2,3</td>
+ <td>5-10-2006</td>
+ </tr>
+ <tr>
+ <td>29</td>
+ <td>HZI1041</td>
+ <td>DBA/2Jf (f27) CD25+</td>
+ <td>F</td>
+ <td>DBA/2J</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>DBA/2Jf</td>
+ <td>16</td>
+ <td>f27</td>
+ <td>5,6,7</td>
+ <td>5-10-2006</td>
+ </tr>
+ <tr>
+ <td>30</td>
+ <td>HZI1042</td>
+ <td>DBA/2Jm (m21) CD25+</td>
+ <td>M</td>
+ <td>DBA/2J</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>DBA/2Jm</td>
+ <td>21</td>
+ <td>m21</td>
+ <td>1,2,3</td>
+ <td>4-11-2006</td>
+ </tr>
+ <tr>
+ <td>31</td>
+ <td>HZI1487</td>
+ <td>BXD-08f (f67) CD25+</td>
+ <td>F</td>
+ <td>BXD8</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-08f</td>
+ <td>11</td>
+ <td>f67</td>
+ <td>4,5,6</td>
+ <td>6-25-2007</td>
+ </tr>
+ <tr>
+ <td>32</td>
+ <td>HZI1488</td>
+ <td>BXD-08m (m66) CD25+</td>
+ <td>M</td>
+ <td>BXD8</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-08m</td>
+ <td>17</td>
+ <td>m66</td>
+ <td>1,2,3</td>
+ <td>6-25-2007</td>
+ </tr>
+ <tr>
+ <td>33</td>
+ <td>HZI1489</td>
+ <td>BXD-16m (m36) CD25+</td>
+ <td>M</td>
+ <td>BXD16</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-16m</td>
+ <td>20, 16</td>
+ <td>m36</td>
+ <td>5,6,7</td>
+ <td>8-28-2006</td>
+ </tr>
+ <tr>
+ <td>34</td>
+ <td>HZI1490</td>
+ <td>BXD-12m (m42) CD25+</td>
+ <td>M</td>
+ <td>BXD12</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-12m</td>
+ <td>20</td>
+ <td>m42</td>
+ <td>5,6,7</td>
+ <td>10-23-2006</td>
+ </tr>
+ <tr>
+ <td>35</td>
+ <td>HZI1491</td>
+ <td>BXD-13f (f44) CD25+</td>
+ <td>F</td>
+ <td>BXD13</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-13f</td>
+ <td>15</td>
+ <td>f44</td>
+ <td>1,2,3</td>
+ <td>12-13-2006</td>
+ </tr>
+ <tr>
+ <td>36</td>
+ <td>HZI1492</td>
+ <td>BXD-13m (m45) CD25+</td>
+ <td>M</td>
+ <td>BXD13</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-13m</td>
+ <td>15</td>
+ <td>m45</td>
+ <td>4,5,6,7</td>
+ <td>12-13-2006</td>
+ </tr>
+ <tr>
+ <td>37</td>
+ <td>HZI1493</td>
+ <td>BXD-14f (f48) CD25+</td>
+ <td>F</td>
+ <td>BXD14</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-14f</td>
+ <td>16</td>
+ <td>f48</td>
+ <td>5,6,7</td>
+ <td>2-15-2007</td>
+ </tr>
+ <tr>
+ <td>38</td>
+ <td>HZI1494</td>
+ <td>BXD-19f (f64) CD25+</td>
+ <td>F</td>
+ <td>BXD19</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-19f</td>
+ <td>19</td>
+ <td>f64</td>
+ <td>7,8,9</td>
+ <td>6-20-2007</td>
+ </tr>
+ <tr>
+ <td>39</td>
+ <td>HZI1495</td>
+ <td>BXD-19m (m46) CD25+</td>
+ <td>M</td>
+ <td>BXD19</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-19m</td>
+ <td>16</td>
+ <td>m46</td>
+ <td>4,5,6</td>
+ <td>12-15-2006</td>
+ </tr>
+ <tr>
+ <td>40</td>
+ <td>HZI1499</td>
+ <td>BXD-28m (m43) CD25+</td>
+ <td>M</td>
+ <td>BXD28</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-28m</td>
+ <td>17,2</td>
+ <td>m43</td>
+ <td>1,2,3</td>
+ <td>10-23-2006</td>
+ </tr>
+ <tr>
+ <td>41</td>
+ <td>HZI1500</td>
+ <td>BXD-42f (f49) CD25+</td>
+ <td>F</td>
+ <td>BXD42</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-42f</td>
+ <td>17</td>
+ <td>f49</td>
+ <td>??</td>
+ <td>3-8-2007</td>
+ </tr>
+ <tr>
+ <td>42</td>
+ <td>HZI1502</td>
+ <td>F1 (BXD)m (f50) CD25+</td>
+ <td>M</td>
+ <td>B6D2F1</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>F1 (BXD)m</td>
+ <td>15</td>
+ <td>m51</td>
+ <td>1,2,3,</td>
+ <td>4-18-2007</td>
+ </tr>
+ <tr>
+ <td>43</td>
+ <td>HZI1503</td>
+ <td>F1 (BXD)m (m51) CD25+</td>
+ <td>F</td>
+ <td>B6D2F1</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>F1 (BXD)f</td>
+ <td>15</td>
+ <td>f50</td>
+ <td>1,2,3</td>
+ <td>4-18-2007</td>
+ </tr>
+ <tr>
+ <td>44</td>
+ <td>HZI1504</td>
+ <td>BXD-86f (f52) CD25+</td>
+ <td>F</td>
+ <td>BXD86</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-86f</td>
+ <td>16</td>
+ <td>f52</td>
+ <td>1,2,3</td>
+ <td>4-18-2007</td>
+ </tr>
+ <tr>
+ <td>45</td>
+ <td>HZI1505</td>
+ <td>BXD-43f (f53) CD25+</td>
+ <td>F</td>
+ <td>BXD43</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-43f</td>
+ <td>16</td>
+ <td>f53</td>
+ <td>1,2,3</td>
+ <td>4-23-2007</td>
+ </tr>
+ <tr>
+ <td>46</td>
+ <td>HZI1506</td>
+ <td>BXD-44f (f54) CD25+</td>
+ <td>F</td>
+ <td>BXD44</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-44f</td>
+ <td>18</td>
+ <td>f54</td>
+ <td>1,2,3</td>
+ <td>4-23-2007</td>
+ </tr>
+ <tr>
+ <td>47</td>
+ <td>HZI1507</td>
+ <td>BXD-45f (f55) CD25+</td>
+ <td>F</td>
+ <td>BXD45</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-45f</td>
+ <td>19</td>
+ <td>f55</td>
+ <td>1,2,3</td>
+ <td>4-23-2007</td>
+ </tr>
+ <tr>
+ <td>48</td>
+ <td>HZI1508</td>
+ <td>BXD-62f (f56) CD25+</td>
+ <td>F</td>
+ <td>BXD62</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-62f</td>
+ <td>17</td>
+ <td>f56</td>
+ <td>1,2,3</td>
+ <td>4-26-2007</td>
+ </tr>
+ <tr>
+ <td>49</td>
+ <td>HZI1509</td>
+ <td>BXD-73f (f57) CD25+</td>
+ <td>F</td>
+ <td>BXD73</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-73f</td>
+ <td>18</td>
+ <td>f57</td>
+ <td>1,2,3</td>
+ <td>4-26-2007</td>
+ </tr>
+ <tr>
+ <td>50</td>
+ <td>HZI1510</td>
+ <td>BXD-51f (f59) CD25+</td>
+ <td>F</td>
+ <td>BXD51</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-51f</td>
+ <td>22</td>
+ <td>f59</td>
+ <td>1,2,3</td>
+ <td>6-18-2007</td>
+ </tr>
+ <tr>
+ <td>51</td>
+ <td>HZI1523</td>
+ <td>BXD-75f (f58) CD25+</td>
+ <td>F</td>
+ <td>BXD75</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-75f</td>
+ <td>15,17</td>
+ <td>f58</td>
+ <td>1,2,3</td>
+ <td>4-26-2007</td>
+ </tr>
+ <tr>
+ <td>52</td>
+ <td>HZI1525</td>
+ <td>BXD-29m (m37) CD25+</td>
+ <td>M</td>
+ <td>BXD29</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-29m</td>
+ <td>20, 16</td>
+ <td>m37</td>
+ <td>1,2,3</td>
+ <td>8-29-2006</td>
+ </tr>
+ <tr>
+ <td>53</td>
+ <td>HZI1526</td>
+ <td>BXD-34f (f4) CD25+</td>
+ <td>F</td>
+ <td>BXD34</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-34f</td>
+ <td>17</td>
+ <td>f4</td>
+ <td>1,2,3</td>
+ <td>2-1-2006</td>
+ </tr>
+ <tr>
+ <td>54</td>
+ <td>HZI1940</td>
+ <td>BXD-27m (m39) CD25+</td>
+ <td>M</td>
+ <td>BXD27</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-27m</td>
+ <td>18 - 20</td>
+ <td>m39</td>
+ <td>1,3,4</td>
+ <td>9-1-2006</td>
+ </tr>
+ <tr>
+ <td>55</td>
+ <td>HZI1941</td>
+ <td>BXD-42m (m47) CD25+</td>
+ <td>M</td>
+ <td>BXD42</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-42m</td>
+ <td>15,16</td>
+ <td>m47</td>
+ <td>1,2,3</td>
+ <td>12-15-2006</td>
+ </tr>
+ <tr>
+ <td>56</td>
+ <td>HZI1942</td>
+ <td>BXD-34m (m5) CD25+</td>
+ <td>M</td>
+ <td>BXD34</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-34m</td>
+ <td>17</td>
+ <td>m5</td>
+ <td>5,7,8</td>
+ <td>2-1-2006</td>
+ </tr>
+ <tr>
+ <td>57</td>
+ <td>HZI1943</td>
+ <td>BXD-38f (f70) CD25+</td>
+ <td>F</td>
+ <td>BXD38</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-38f</td>
+ <td>13</td>
+ <td>f70</td>
+ <td>4,5,6,7</td>
+ <td>2-1-2008</td>
+ </tr>
+ <tr>
+ <td>58</td>
+ <td>HZI1944</td>
+ <td>BXD-31m (m69) CD25+</td>
+ <td>M</td>
+ <td>BXD31</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-31m</td>
+ <td>14</td>
+ <td>m69</td>
+ <td>4,5,6</td>
+ <td>2-1-2008</td>
+ </tr>
+ <tr>
+ <td>59</td>
+ <td>HZI1945</td>
+ <td>BXD-27f (f12) CD25+</td>
+ <td>F</td>
+ <td>BXD27</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-27f</td>
+ <td>18</td>
+ <td>f12</td>
+ <td>1,2</td>
+ <td>2-15-2006</td>
+ </tr>
+ <tr>
+ <td>60</td>
+ <td>HZI1946</td>
+ <td>BXD-38m (m63) CD25+</td>
+ <td>M</td>
+ <td>BXD38</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-38m</td>
+ <td>18</td>
+ <td>m63</td>
+ <td>1,2,3</td>
+ <td>6-20-2007</td>
+ </tr>
+ <tr>
+ <td>61</td>
+ <td>HZI1947</td>
+ <td>BXD-23f (f62) CD25+</td>
+ <td>F</td>
+ <td>BXD23</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-23f</td>
+ <td>21</td>
+ <td>f62</td>
+ <td>1,2,3</td>
+ <td>6-20-2007</td>
+ </tr>
+ <tr>
+ <td>62</td>
+ <td>HZI1948</td>
+ <td>BXD-28f (f61) CD25+</td>
+ <td>F</td>
+ <td>BXD28</td>
+ <td>CD25+</td>
+ <td>Yes</td>
+ <td>BXD-28f</td>
+ <td>22</td>
+ <td>f61</td>
+ <td>1,2,3</td>
+ <td>6-18-2007</td>
+ </tr>
+ </tbody>
+ </table>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</blockquote>
+</blockquote>
diff --git a/general/datasets/RTC_1106_R/experiment-design.rtf b/general/datasets/RTC_1106_R/experiment-design.rtf new file mode 100644 index 0000000..a69dffc --- /dev/null +++ b/general/datasets/RTC_1106_R/experiment-design.rtf @@ -0,0 +1,7 @@ +<blockquote>
+<p>Parental and BXD lines were received from Jackson Laboratory, or from Oak Ridge Laboratory (BXD43, BXD51, BXD61, BXD62, BXD65, BXD68, BXD69, BXD73, BXD75, BXD87, BXD90), and were bred in the facility of the Neuro-BSIK consortium (VU University Amsterdam). Female mice, 3 per strain, were housed on sawdust in standard Makrolon type II cages with food (Harlan Teklad 2018) and water ad libitum under specific pathogen free conditions. For the analysis, mice were transferred to the animal facility in Braunschweig and adapted for at least two weeks to the new environment before preparing the spleen cells. All protocols involving mice were approved by national animal welfare committees.</p>
+
+<p>For sorting of Tregs and Th cells, splenocytes from 31 BXD recombinant inbred strains, as well as from the parental strains DBA/2J and C57BL/6J, were isolated by flushing the spleens with erythrocyte lysis buffer. Cells were collected by centrifugation, resuspended in cold FACS-buffer (PBS / 2% FCS / 0,5 mM EDTA). After passing the cells through a 100 µm cell strainer and an additional washing step with FACS-buffer, splenocytes were stained with anti-CD4-APC and anti-CD25-PE for 10 minutes at 4 °C, washed and resuspended in FACS-buffer. CD4+ T cells were separated into CD4+CD25+ Tregs and CD4+CD25- Th cells using a MoFlo cell sorter (Cytomation) and purity of the sorted T cell subsets reached 95-97%.</p>
+
+<p>Quality and integrity of the total RNA isolated from 1x10<sup>5</sup> cells was controlled by running all samples on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). RNA amplification and labeling was done according to manufactures protocol (Small Sample Target Labeling Assay Version II, Affymetrix; Santa Clara, CA). The concentration of biotin-labeled cRNA was determined by UV absorbance. In all cases, 10 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix MOE430 2.0 for 16 hours at 46 °C. After hybridisation the GeneChips were washed and stained using the Affymetrix´s recommended EukGE-WS2v5 protocol for GeneChip Fluidics FS400 station. Images were scanned using GeneChip Scanner 3000 under the control of GCOS 1.3 software package (Affymetrix; Santa Clara, CA).</p>
+</blockquote>
diff --git a/general/datasets/RTC_1106_R/notes.rtf b/general/datasets/RTC_1106_R/notes.rtf new file mode 100644 index 0000000..dbd0c60 --- /dev/null +++ b/general/datasets/RTC_1106_R/notes.rtf @@ -0,0 +1 @@ +<p>This text file was generated by KS on July, 18 2011.</p>
diff --git a/general/datasets/RTC_1106_R/platform.rtf b/general/datasets/RTC_1106_R/platform.rtf new file mode 100644 index 0000000..ed42a9b --- /dev/null +++ b/general/datasets/RTC_1106_R/platform.rtf @@ -0,0 +1,3 @@ +<blockquote>
+<p>The Affymetrix M430 2.0 array consists of approximately 992,936 useful 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts, including a majority of known genes and expressed sequence tags. The array sequences were selected late in 2002 using NCBI Build 107 by Affymetrix. The UTHSC GN group continuously reannotated probe sets on this array, producing more accurate data on probe and probe set targets. All probes have also be aligned to the most recent assembly of the Mouse Genome using Jim Kent's BLAT program.</p>
+</blockquote>
diff --git a/general/datasets/RTC_1106_R/processing.rtf b/general/datasets/RTC_1106_R/processing.rtf new file mode 100644 index 0000000..b8d49b7 --- /dev/null +++ b/general/datasets/RTC_1106_R/processing.rtf @@ -0,0 +1,6 @@ +<blockquote>
+<p>Microarray data then was preprocessed using the RMA method [bolstad] and subsequently batch corrected [Alberts et al]. In this study, RNA was extracted at three different points in time for the Treg samples and also microarray processing was performed at three different points in time. Similarly, the Th samples were processed in two batches. Therefore, we performed a batch correction for both cell types using the following ANOVA model before further analysis of the data.<br />
+<em>y<sub>i</sub> = </em><em>μ</em><em> + B<sub>i</sub> + e<sub>i</sub></em><br />
+Where <em>y<sub>i</sub></em> is the expression level of the <em>i</em><sup>th</sup> microarray, <em>μ</em> is the overall mean, B<em><sub>i</sub> </em>is the batch to which the <em>i</em>th individual belongs and <em>e<sub>i</sub> </em>is the residual error.<br />
+Batch corrected data sets were then preprocessed before transferring them to the GeneNetwork (GN) database: Adding an offset of 1 unit to each signal intensity value to ensure that the logarithm of all values were positive, computing the log2 value, performing a quantile normalization of the log2 values for the total set of arrays using the same initial steps used by the RMA transform, computing the Z scores for each cell value, multiplying all Z scores by 2 and adding 8 to the value of all Z scores. The advantage of this variant of a Z transformation is that all values are positive and that 1 unit represents approximately a 2-fold difference in expression as determined using the spike-in control probe sets. The mean values were subsequently calculated if multiple samples from one BXD line were recorded (male and females or replicates).</p>
+</blockquote>
diff --git a/general/datasets/RTC_1106_R/summary.rtf b/general/datasets/RTC_1106_R/summary.rtf new file mode 100644 index 0000000..2094b06 --- /dev/null +++ b/general/datasets/RTC_1106_R/summary.rtf @@ -0,0 +1,3 @@ +<blockquote>ERROR-CHECKED FIRST PHASE PRIVATE TEST DATA SET. This data set provides estimates of gene expression in <a class="fs14" href="http://en.wikipedia.org/wiki/Regulatory_T_cell" target="_empty">regulatory T cells</a> (CD4+CD25+) of BXD strains. Data were generated by Prof. Dr. Klaus Schughart and colleagues at the <a class="fs14" href="http://www.helmholtz-hzi.de/en/" target="_empty">Helmholtz Centre for Infection Research (HZI)</a>. Samples were processed using a total of 35 Affymetrix MOE 430 2.0 short oligomer microarrays, of which 33 passed stringent quality control and error checking.
+<p>This is a private test data set. Please contact Dr. Klaus Schughart for early access.</p>
+</blockquote>
|