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Diffstat (limited to 'general/datasets/Ut_ceph_rankinv0909')
8 files changed, 2043 insertions, 0 deletions
diff --git a/general/datasets/Ut_ceph_rankinv0909/acknowledgment.rtf b/general/datasets/Ut_ceph_rankinv0909/acknowledgment.rtf new file mode 100644 index 0000000..7d66250 --- /dev/null +++ b/general/datasets/Ut_ceph_rankinv0909/acknowledgment.rtf @@ -0,0 +1 @@ +<p>Financial support for this project was provided by Dr. Barrett Haik and the Hamilton Eye Institute, by NIH grant support to Malak Kotb, Robert W. Williams, Rita G. Kasal and colleagues, and by the UT Center for Integrative and Translational Genomics.</p>
diff --git a/general/datasets/Ut_ceph_rankinv0909/cases.rtf b/general/datasets/Ut_ceph_rankinv0909/cases.rtf new file mode 100644 index 0000000..f4f6663 --- /dev/null +++ b/general/datasets/Ut_ceph_rankinv0909/cases.rtf @@ -0,0 +1,2009 @@ +<p><strong>About the CEPH/UTAH families used to generate this data set:</strong></p>
+
+<p>The CEPH/UTAH families used in this data set are part of CEPH repository linkage families of National Institute of General Medical Sciences (NIGMS) human genetic cell repository. These are immortalized human B-lymphocytes (EBV-transformed) from Caucasian donors of UTAH/Mormon ethnicity. The CEPH/UTAH families contain 48 families; the present data set includes 14 of these families with available DNA/genotypes for each member of these pedigrees. There are five families common with the published Monks et al (2004), namely families: 1346, 1362, 1418, 1421, and 1424.</p>
+
+<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>Repository<br />
+ Number</td>
+ <td>Case ID</td>
+ <td>Gender</td>
+ <td>Family ID</td>
+ <td>Family Member ID</td>
+ <td>Sentrix ID</td>
+ <td>Sentrix<br />
+ Position</td>
+ <td>Batch ID</td>
+ </tr>
+ <tr>
+ <td>1</td>
+ <td>GM07038</td>
+ <td>1333001</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>1</td>
+ <td>4256249060</td>
+ <td>A</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>2</td>
+ <td>GM06987</td>
+ <td>1333002</td>
+ <td>Female</td>
+ <td>1333</td>
+ <td>2</td>
+ <td>4158260019</td>
+ <td>B</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>3</td>
+ <td>GM07004</td>
+ <td>1333003</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>3</td>
+ <td>4256249103</td>
+ <td>A</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>4</td>
+ <td>GM07052</td>
+ <td>1333004</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>4</td>
+ <td>4256249051</td>
+ <td>A</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>5</td>
+ <td>GM06982</td>
+ <td>1333005</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>5</td>
+ <td>4158260009</td>
+ <td>F</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>6</td>
+ <td>GM07011</td>
+ <td>1333006</td>
+ <td>Female</td>
+ <td>1333</td>
+ <td>6</td>
+ <td>4158260012</td>
+ <td>C</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>7</td>
+ <td>GM07009</td>
+ <td>1333007</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>7</td>
+ <td>4256249101</td>
+ <td>F</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>8</td>
+ <td>GM07678</td>
+ <td>1333008</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>8</td>
+ <td>4158260005</td>
+ <td>B</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>9</td>
+ <td>GM07026</td>
+ <td>1333009</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>9</td>
+ <td>4158260026</td>
+ <td>C</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>10</td>
+ <td>GM07679</td>
+ <td>1333010</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>10</td>
+ <td>4158260030</td>
+ <td>C</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>11</td>
+ <td>GM07049</td>
+ <td>1333011</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>11</td>
+ <td>4256249059</td>
+ <td>A</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>12</td>
+ <td>GM07002</td>
+ <td>1333012</td>
+ <td>Female</td>
+ <td>1333</td>
+ <td>12</td>
+ <td>4158260001</td>
+ <td>B</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>13</td>
+ <td>GM07017</td>
+ <td>1333013</td>
+ <td>Male</td>
+ <td>1333</td>
+ <td>13</td>
+ <td>4158260027</td>
+ <td>B</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>14</td>
+ <td>GM07341</td>
+ <td>1333014</td>
+ <td>Female</td>
+ <td>1333</td>
+ <td>14</td>
+ <td>4256249042</td>
+ <td>A</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>15</td>
+ <td>GM11820</td>
+ <td>1333015</td>
+ <td>Female</td>
+ <td>1333</td>
+ <td>15</td>
+ <td>4256249104</td>
+ <td>E</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>16</td>
+ <td>GM07048</td>
+ <td>1341001</td>
+ <td>Male</td>
+ <td>1341</td>
+ <td>1</td>
+ <td>4256249103</td>
+ <td>B</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>17</td>
+ <td>GM06991</td>
+ <td>1341002</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>2</td>
+ <td>4158260027</td>
+ <td>A</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>18</td>
+ <td>GM07343</td>
+ <td>1341003</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>3</td>
+ <td>4256249095</td>
+ <td>C</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>19</td>
+ <td>GM07044</td>
+ <td>1341004</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>4</td>
+ <td>4158260002</td>
+ <td>C</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>20</td>
+ <td>GM07012</td>
+ <td>1341005</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>5</td>
+ <td>4158260026</td>
+ <td>D</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>21</td>
+ <td>GM07344</td>
+ <td>1341006</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>6</td>
+ <td>4158260030</td>
+ <td>B</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>22</td>
+ <td>GM07021</td>
+ <td>1341007</td>
+ <td>Male</td>
+ <td>1341</td>
+ <td>7</td>
+ <td>4256249097</td>
+ <td>B</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>23</td>
+ <td>GM07006</td>
+ <td>1341008</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>8</td>
+ <td>4158260001</td>
+ <td>C</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>24</td>
+ <td>GM07010</td>
+ <td>1341009</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>9</td>
+ <td>41582600011</td>
+ <td>A</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>25</td>
+ <td>GM07020</td>
+ <td>1341010</td>
+ <td>Male</td>
+ <td>1341</td>
+ <td>10</td>
+ <td>4158260007</td>
+ <td>A</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>26</td>
+ <td>GM07034</td>
+ <td>1341011</td>
+ <td>Male</td>
+ <td>1341</td>
+ <td>11</td>
+ <td>4158260007</td>
+ <td>B</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>27</td>
+ <td>GM07055</td>
+ <td>1341012</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>12</td>
+ <td>4158260012</td>
+ <td>E</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>28</td>
+ <td>GM06993</td>
+ <td>1341013</td>
+ <td>Male</td>
+ <td>1341</td>
+ <td>13</td>
+ <td>4256249059</td>
+ <td>C</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>29</td>
+ <td>GM06985</td>
+ <td>1341014</td>
+ <td>Female</td>
+ <td>1341</td>
+ <td>14</td>
+ <td>4158260007</td>
+ <td>C</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>30</td>
+ <td>GM10852</td>
+ <td>1346002</td>
+ <td>Female</td>
+ <td>1346</td>
+ <td>2</td>
+ <td>4256249098</td>
+ <td>D</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>31</td>
+ <td>GM12035</td>
+ <td>1346003</td>
+ <td>Male</td>
+ <td>1346</td>
+ <td>3</td>
+ <td>4158260007</td>
+ <td>D</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>32</td>
+ <td>GM12036</td>
+ <td>1346004</td>
+ <td>Male</td>
+ <td>1346</td>
+ <td>4</td>
+ <td>4256249047</td>
+ <td>A</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>33</td>
+ <td>GM12037</td>
+ <td>1346005</td>
+ <td>Male</td>
+ <td>1346</td>
+ <td>5</td>
+ <td>4158260027</td>
+ <td>E</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>34</td>
+ <td>GM12038</td>
+ <td>1346006</td>
+ <td>Male</td>
+ <td>1346</td>
+ <td>6</td>
+ <td>4158260001</td>
+ <td>E</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>35</td>
+ <td>GM12039</td>
+ <td>1346007</td>
+ <td>Male</td>
+ <td>1346</td>
+ <td>7</td>
+ <td>4256249097</td>
+ <td>C</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>36</td>
+ <td>GM12041</td>
+ <td>1346009</td>
+ <td>Female</td>
+ <td>1346</td>
+ <td>9</td>
+ <td>4256249099</td>
+ <td>B</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>37</td>
+ <td>GM12042</td>
+ <td>1346010</td>
+ <td>Female</td>
+ <td>1346</td>
+ <td>10</td>
+ <td>41582600011</td>
+ <td>D</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>38</td>
+ <td>GM12043</td>
+ <td>1346011</td>
+ <td>Male</td>
+ <td>1346</td>
+ <td>11</td>
+ <td>4158260007</td>
+ <td>E</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>39</td>
+ <td>GM12044</td>
+ <td>1346012</td>
+ <td>Female</td>
+ <td>1346</td>
+ <td>12</td>
+ <td>4256249096</td>
+ <td>F</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>40</td>
+ <td>GM12046</td>
+ <td>1346014</td>
+ <td>Female</td>
+ <td>1346</td>
+ <td>14</td>
+ <td>4158260007</td>
+ <td>F</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>41</td>
+ <td>GM10858</td>
+ <td>1347001</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>1</td>
+ <td>4158260030</td>
+ <td>A</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>42</td>
+ <td>GM10859</td>
+ <td>1347002</td>
+ <td>Female</td>
+ <td>1347</td>
+ <td>2</td>
+ <td>4158260027</td>
+ <td>C</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>43</td>
+ <td>GM11870</td>
+ <td>1347003</td>
+ <td>Female</td>
+ <td>1347</td>
+ <td>3</td>
+ <td>4158260018</td>
+ <td>C</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>44</td>
+ <td>GM11871</td>
+ <td>1347004</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>4</td>
+ <td>4256249060</td>
+ <td>B</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>45</td>
+ <td>GM11872</td>
+ <td>1347005</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>5</td>
+ <td>4256249097</td>
+ <td>A</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>46</td>
+ <td>GM11873</td>
+ <td>1347006</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>6</td>
+ <td>4158260001</td>
+ <td>A</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>47</td>
+ <td>GM11875</td>
+ <td>1347008</td>
+ <td>Female</td>
+ <td>1347</td>
+ <td>8</td>
+ <td>4256249095</td>
+ <td>E</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>48</td>
+ <td>GM11876</td>
+ <td>1347009</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>9</td>
+ <td>4256249059</td>
+ <td>E</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>49</td>
+ <td>GM11877</td>
+ <td>1347010</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>10</td>
+ <td>4158260021</td>
+ <td>A</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>50</td>
+ <td>GM11878</td>
+ <td>1347011</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>11</td>
+ <td>4158260008</td>
+ <td>A</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>51</td>
+ <td>GM11879</td>
+ <td>1347012</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>12</td>
+ <td>4158260019</td>
+ <td>D</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>52</td>
+ <td>GM11880</td>
+ <td>1347013</td>
+ <td>Female</td>
+ <td>1347</td>
+ <td>13</td>
+ <td>4158260008</td>
+ <td>B</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>53</td>
+ <td>GM11881</td>
+ <td>1347014</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>14</td>
+ <td>4256249101</td>
+ <td>C</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>54</td>
+ <td>GM11882</td>
+ <td>1347015</td>
+ <td>Female</td>
+ <td>1347</td>
+ <td>15</td>
+ <td>4158260008</td>
+ <td>C</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>55</td>
+ <td>GM11883</td>
+ <td>1347016</td>
+ <td>Male</td>
+ <td>1347</td>
+ <td>16</td>
+ <td>41582600011</td>
+ <td>B</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>56</td>
+ <td>GM10860</td>
+ <td>1362001</td>
+ <td>Male</td>
+ <td>1362</td>
+ <td>1</td>
+ <td>4256249097</td>
+ <td>E</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>57</td>
+ <td>GM10861</td>
+ <td>1362002</td>
+ <td>Female</td>
+ <td>1362</td>
+ <td>2</td>
+ <td>4158260027</td>
+ <td>D</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>58</td>
+ <td>GM11982</td>
+ <td>1362003</td>
+ <td>Female</td>
+ <td>1362</td>
+ <td>3</td>
+ <td>4158260019</td>
+ <td>F</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>59</td>
+ <td>GM11983</td>
+ <td>1362004</td>
+ <td>Female</td>
+ <td>1362</td>
+ <td>4</td>
+ <td>4158260030</td>
+ <td>D</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>60</td>
+ <td>GM11984</td>
+ <td>1362005</td>
+ <td>Male</td>
+ <td>1362</td>
+ <td>5</td>
+ <td>4158260008</td>
+ <td>D</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>61</td>
+ <td>GM11985</td>
+ <td>1362006</td>
+ <td>Female</td>
+ <td>1362</td>
+ <td>6</td>
+ <td>4158260002</td>
+ <td>F</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>62</td>
+ <td>GM11986</td>
+ <td>1362007</td>
+ <td>Female</td>
+ <td>1362</td>
+ <td>7</td>
+ <td>4256249060</td>
+ <td>C</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>63</td>
+ <td>GM11987</td>
+ <td>1362008</td>
+ <td>Male</td>
+ <td>1362</td>
+ <td>8</td>
+ <td>4158260005</td>
+ <td>F</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>64</td>
+ <td>GM11988</td>
+ <td>1362009</td>
+ <td>Female</td>
+ <td>1362</td>
+ <td>9</td>
+ <td>4256249042</td>
+ <td>B</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>65</td>
+ <td>GM11989</td>
+ <td>1362010</td>
+ <td>Female</td>
+ <td>1362</td>
+ <td>10</td>
+ <td>4158260001</td>
+ <td>F</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>66</td>
+ <td>GM11990</td>
+ <td>1362011</td>
+ <td>Male</td>
+ <td>1362</td>
+ <td>11</td>
+ <td>4256249094</td>
+ <td>A</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>67</td>
+ <td>GM11991</td>
+ <td>1362012</td>
+ <td>Female</td>
+ <td>1362</td>
+ <td>12</td>
+ <td>4158260018</td>
+ <td>E</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>68</td>
+ <td>GM11992</td>
+ <td>1362013</td>
+ <td>Male</td>
+ <td>1362</td>
+ <td>13</td>
+ <td>4256249059</td>
+ <td>B</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>69</td>
+ <td>GM11993</td>
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+ <td>4256249059</td>
+ <td>F</td>
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+ <td>143</td>
+ <td>GM12764</td>
+ <td>1447013</td>
+ <td>Male</td>
+ <td>1447</td>
+ <td>13</td>
+ <td>4256249042</td>
+ <td>E</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>144</td>
+ <td>GM12765</td>
+ <td>1447014</td>
+ <td>Male</td>
+ <td>1447</td>
+ <td>14</td>
+ <td>4158260026</td>
+ <td>A</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>145</td>
+ <td>GM12766</td>
+ <td>1451001</td>
+ <td>Male</td>
+ <td>1451</td>
+ <td>1</td>
+ <td>4158260009</td>
+ <td>B</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>146</td>
+ <td>GM12767</td>
+ <td>1451002</td>
+ <td>Female</td>
+ <td>1451</td>
+ <td>2</td>
+ <td>4158260012</td>
+ <td>B</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>147</td>
+ <td>GM12768</td>
+ <td>1451003</td>
+ <td>Male</td>
+ <td>1451</td>
+ <td>3</td>
+ <td>4256249041</td>
+ <td>D</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>148</td>
+ <td>GM12769</td>
+ <td>1451004</td>
+ <td>Female</td>
+ <td>1451</td>
+ <td>4</td>
+ <td>4158260021</td>
+ <td>F</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>149</td>
+ <td>GM12770</td>
+ <td>1451005</td>
+ <td>Female</td>
+ <td>1451</td>
+ <td>5</td>
+ <td>4158260005</td>
+ <td>A</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>150</td>
+ <td>GM12771</td>
+ <td>1451006</td>
+ <td>Male</td>
+ <td>1451</td>
+ <td>6</td>
+ <td>4256249047</td>
+ <td>E</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>151</td>
+ <td>GM12772</td>
+ <td>1451007</td>
+ <td>Female</td>
+ <td>1451</td>
+ <td>7</td>
+ <td>4158260019</td>
+ <td>A</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>152</td>
+ <td>GM12773</td>
+ <td>1451008</td>
+ <td>Female</td>
+ <td>1451</td>
+ <td>8</td>
+ <td>4158260002</td>
+ <td>B</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>153</td>
+ <td>GM12848</td>
+ <td>1451009</td>
+ <td>Female</td>
+ <td>1451</td>
+ <td>9</td>
+ <td>4256249051</td>
+ <td>D</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>154</td>
+ <td>GM12774</td>
+ <td>1451010</td>
+ <td>Male</td>
+ <td>1451</td>
+ <td>10</td>
+ <td>4158260030</td>
+ <td>F</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>155</td>
+ <td>GM12776</td>
+ <td>1451012</td>
+ <td>Female</td>
+ <td>1451</td>
+ <td>12</td>
+ <td>4256249099</td>
+ <td>E</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>156</td>
+ <td>GM12777</td>
+ <td>1451013</td>
+ <td>Male</td>
+ <td>1451</td>
+ <td>13</td>
+ <td>4256249060</td>
+ <td>D</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>157</td>
+ <td>GM12801</td>
+ <td>1454001</td>
+ <td>Male</td>
+ <td>1454</td>
+ <td>1</td>
+ <td>4256249103</td>
+ <td>C</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>158</td>
+ <td>GM12803</td>
+ <td>1454003</td>
+ <td>Female</td>
+ <td>1454</td>
+ <td>3</td>
+ <td>4158260019</td>
+ <td>C</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>159</td>
+ <td>GM12804</td>
+ <td>1454004</td>
+ <td>Female</td>
+ <td>1454</td>
+ <td>4</td>
+ <td>4256249101</td>
+ <td>D</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>160</td>
+ <td>GM12805</td>
+ <td>1454005</td>
+ <td>Male</td>
+ <td>1454</td>
+ <td>5</td>
+ <td>4256249095</td>
+ <td>F</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>161</td>
+ <td>GM12806</td>
+ <td>1454006</td>
+ <td>Male</td>
+ <td>1454</td>
+ <td>6</td>
+ <td>4256249098</td>
+ <td>E</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>162</td>
+ <td>GM12808</td>
+ <td>1454008</td>
+ <td>Female</td>
+ <td>1454</td>
+ <td>8</td>
+ <td>4256249099</td>
+ <td>C</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>163</td>
+ <td>GM12809</td>
+ <td>1454009</td>
+ <td>Female</td>
+ <td>1454</td>
+ <td>9</td>
+ <td>4256249051</td>
+ <td>E</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>164</td>
+ <td>GM12810</td>
+ <td>1454010</td>
+ <td>Male</td>
+ <td>1454</td>
+ <td>10</td>
+ <td>4256249104</td>
+ <td>A</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>165</td>
+ <td>GM12811</td>
+ <td>1454011</td>
+ <td>Male</td>
+ <td>1454</td>
+ <td>11</td>
+ <td>4256249044</td>
+ <td>B</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>166</td>
+ <td>GM12812</td>
+ <td>1454012</td>
+ <td>Male</td>
+ <td>1454</td>
+ <td>12</td>
+ <td>4256249042</td>
+ <td>F</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>167</td>
+ <td>GM12813</td>
+ <td>1454013</td>
+ <td>Female</td>
+ <td>1454</td>
+ <td>13</td>
+ <td>4256249094</td>
+ <td>E</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>168</td>
+ <td>GM12814</td>
+ <td>1454014</td>
+ <td>Male</td>
+ <td>1454</td>
+ <td>14</td>
+ <td>4256249096</td>
+ <td>D</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>169</td>
+ <td>GM12815</td>
+ <td>1454015</td>
+ <td>Female</td>
+ <td>1454</td>
+ <td>15</td>
+ <td>4256249041</td>
+ <td>E</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>170</td>
+ <td>GM12816</td>
+ <td>1454016</td>
+ <td>Male</td>
+ <td>1454</td>
+ <td>16</td>
+ <td>4256249047</td>
+ <td>F</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>171</td>
+ <td>GM12817</td>
+ <td>1456001</td>
+ <td>Male</td>
+ <td>1456</td>
+ <td>1</td>
+ <td>4256249051</td>
+ <td>F</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>172</td>
+ <td>GM12818</td>
+ <td>1456002</td>
+ <td>Female</td>
+ <td>1456</td>
+ <td>2</td>
+ <td>4256249101</td>
+ <td>E</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>173</td>
+ <td>GM12819</td>
+ <td>1456003</td>
+ <td>Male</td>
+ <td>1456</td>
+ <td>3</td>
+ <td>4256249095</td>
+ <td>B</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>174</td>
+ <td>GM12821</td>
+ <td>1456005</td>
+ <td>Female</td>
+ <td>1456</td>
+ <td>5</td>
+ <td>4256249044</td>
+ <td>C</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>175</td>
+ <td>GM12822</td>
+ <td>1456006</td>
+ <td>Male</td>
+ <td>1456</td>
+ <td>6</td>
+ <td>4256249094</td>
+ <td>F</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>176</td>
+ <td>GM12823</td>
+ <td>1456007</td>
+ <td>Male</td>
+ <td>1456</td>
+ <td>7</td>
+ <td>4256249096</td>
+ <td>B</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>177</td>
+ <td>GM12824</td>
+ <td>1456008</td>
+ <td>Female</td>
+ <td>1456</td>
+ <td>8</td>
+ <td>4256249104</td>
+ <td>D</td>
+ <td>7</td>
+ </tr>
+ <tr>
+ <td>178</td>
+ <td>GM12825</td>
+ <td>1456009</td>
+ <td>Male</td>
+ <td>1456</td>
+ <td>9</td>
+ <td>4158260026</td>
+ <td>B</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>179</td>
+ <td>GM12826</td>
+ <td>1456010</td>
+ <td>Female</td>
+ <td>1456</td>
+ <td>10</td>
+ <td>4256249041</td>
+ <td>F</td>
+ <td>6</td>
+ </tr>
+ <tr>
+ <td>180</td>
+ <td>GM12828</td>
+ <td>1456012</td>
+ <td>Female</td>
+ <td>1456</td>
+ <td>12</td>
+ <td>4256249099</td>
+ <td>F</td>
+ <td>7</td>
+ </tr>
+ </tbody>
+ </table>
+ </td>
+ </tr>
+ </tbody>
+</table>
diff --git a/general/datasets/Ut_ceph_rankinv0909/contributors.rtf b/general/datasets/Ut_ceph_rankinv0909/contributors.rtf new file mode 100644 index 0000000..507f2f7 --- /dev/null +++ b/general/datasets/Ut_ceph_rankinv0909/contributors.rtf @@ -0,0 +1,3 @@ +<p>Eldon Geisert, Barrett Haik, Malak Kotb, Lu Lu, Roel Ophoff, Robert Williams.</p>
+
+<p><a href="http://ccr.coriell.org/nigms/ceph/ceph.html" target="_blank">NIGMS Human Genetic Cell Repository</a></p>
diff --git a/general/datasets/Ut_ceph_rankinv0909/experiment-design.rtf b/general/datasets/Ut_ceph_rankinv0909/experiment-design.rtf new file mode 100644 index 0000000..d525b2e --- /dev/null +++ b/general/datasets/Ut_ceph_rankinv0909/experiment-design.rtf @@ -0,0 +1,13 @@ +<p><strong>Experimental Design and Batch Structure:</strong></p>
+
+<p>This data set consists of arrays processed in seven groups. Groups consisted of 2, 3, 4, 4, 3, 6, and then 8 beadchips at a time, batch IDs are indicated in table 1. Samples from same family were scattered among array groups, with samples from six different families were run on one chip. This was done to ensure balance and to minimize batch effects and group-by-family statistical confounds in normalization. This was done with the exception of the first two chips, which were run with 3 generations of the same family on one chip. A single operator, Yan Jiao, processed all arrays using illumina protocol for hybridization, washing and scanning. All samples in a group were labeled on one day, hybridization station accommodates up to 24 samples, or 4 beadchips. Chips were scanned using BeadArray Reader in sets of three.</p>
+
+<p><strong>About the processing of cell lines:</strong></p>
+
+<p>CEPH/UTAH families cell lines were purchased from Coriell repository of cell lines part of NIGMS. Upon arrival from the Coriell institute, we incubated the cell lines in 25ml flasks upright overnight at 37 ºC humidified incubator, with 5% carbon dioxide. We maintained the cells at a density of 5 X 10<sup>5</sup> cells/ml. The composition of the media used was RPMI-1640, 15% fetal bovine serum (FBS) and 2mM L-Glutamine; all FBS used was from the same lot. At 48 hours or when cell counts were ≥ 8 x 10<sup>6</sup> cells total, we harvested the cells and tested each cell line for mycoplasma contamination using e-Myco Mycoplasma PCR detection kit (iNtRON Biotechnology) according to manufacturer protocol. Cell lysates free of mycoplasma were used for RNA extraction as detailed below. We froze duplicates of each cell line at a concentration of ~2–6 x10<sup>6</sup> cells/ml according to standard procedures and stored in liquid nitrogen.</p>
+
+<p><strong>About RNA processing:</strong></p>
+
+<p>Two hundred and five cell lines were used for isolation of RNA. Ms. Sarah Rowe Hasty performed initial RNA isolation, purification and re-precipitation from 205 cell lines in Dr. Malak Kotb laboratory at VAMC. After initial RNA isolation, Ms. Nourtan Abdeltawab treated all samples for removal of contaminating DNA, along with further purification and re-precipitation of all samples. RNA samples that passed quality control were used to generate cRNA samples, those that didn't pass QC were re-extracted as we had duplicates of all cell lines lysates. RNA Extraction details: We used Qiagen RNeasy Mini purification of total RNA from tissues and cells spin protocol. RNA was isolated from 7.5 X 10<sup>5</sup> cells in duplicates. We froze cell lysates in RLT buffer and ß-mercaptoethanol at -80 ºC in 96 well plates until processed at a later time. We thawed samples, one 96 well plate at a time, and proceeded with RNA isolation steps and resuspended the pellets in RNase-free water. We then treated RNA to remove any DNA contamination using DNase digestion with RNase-free DNase kit (Qiagen) according to manufacturer protocol. RNA was finally purified by re-precipitation using ethanol precipitation using Purescript RNA purification kit (Gentra). Final purified RNA was resuspended in RNase-free water. RNA quality control: RNA samples were checked for RNA purity and integrity. RNA purity was evaluated using the 260/280 and 260/230 absorbance ratios. We used RNA samples with 260/280 ratio values ≥ 1.8 and 260/230 of ≥1.7. In cases were RNA samples did not meet these ratios, the RNA was purified by re-precipitation as above. RNA integrity was assessed using 1% RNA denaturing agrose gels. We required clear sharp bands of 18S and 28S rRNA for all samples compared to a control RNA sample to ensure intactness of rRNA.</p>
+
+<p>All RNA samples were processed by Yan Jiao at Dr. Weikuan Gu’s microarray core facility at VA medical center, Memphis, TN. We used only RNA samples that passed quality control as detailed above and of concentration ≥ 50ng/ul for cRNA synthesis using Illumina TotalPrep RNA amplification kit (Ambion) according to manufacturer protocol. The basic outline of the procedure involves reverse transcription of RNA to synthesize cDNA using oligo (dT) primer, followed by in vitro transcription of purified dsDNA to synthesize amplified biotinylated cRNA (aRNA). We evaluated purified labeled cRNA using same methods as mentioned above for RNA samples. cRNA samples of good quality (passing QC), were then used to hybridize to Illumina Human-6WG v2.0 according to Illumina standard protocols.</p>
diff --git a/general/datasets/Ut_ceph_rankinv0909/experiment-type.rtf b/general/datasets/Ut_ceph_rankinv0909/experiment-type.rtf new file mode 100644 index 0000000..0ef1518 --- /dev/null +++ b/general/datasets/Ut_ceph_rankinv0909/experiment-type.rtf @@ -0,0 +1,6 @@ +<strong>Experimental Design and Batch Structure:</strong> </P>
+</P>This data set consists of arrays processed in seven groups. Groups consisted of 2, 3, 4, 4, 3, 6, and then 8 beadchips at a time, batch IDs are indicated in table 1. Samples from same family were scattered among array groups, with samples from six different families were run on one chip. This was done to ensure balance and to minimize batch effects and group-by-family statistical confounds in normalization. This was done with the exception of the first two chips, which were run with 3 generations of the same family on one chip. A single operator, Yan Jiao, processed all arrays using illumina protocol for hybridization, washing and scanning. All samples in a group were labeled on one day, hybridization station accommodates up to 24 samples, or 4 beadchips. Chips were scanned using BeadArray Reader in sets of three. </P>
+<strong>About the processing of cell lines:</strong></P>
+</P>CEPH/UTAH families cell lines were purchased from Coriell repository of cell lines part of NIGMS. Upon arrival from the Coriell institute, we incubated the cell lines in 25ml flasks upright overnight at 37 ºC humidified incubator, with 5% carbon dioxide. We maintained the cells at a density of 5 X 10<SUP>5</SUP> cells/ml. The composition of the media used was RPMI-1640, 15% fetal bovine serum (FBS) and 2mM L-Glutamine; all FBS used was from the same lot. At 48 hours or when cell counts were ≥ 8 x 10<SUP>6</SUP> cells total, we harvested the cells and tested each cell line for mycoplasma contamination using e-Myco Mycoplasma PCR detection kit (iNtRON Biotechnology) according to manufacturer protocol. Cell lysates free of mycoplasma were used for RNA extraction as detailed below. We froze duplicates of each cell line at a concentration of ~2–6 x10<SUP>6</SUP> cells/ml according to standard procedures and stored in liquid nitrogen.</P>
+</P><strong>About RNA processing:</strong></P>
+</P>Two hundred and five cell lines were used for isolation of RNA. Ms. Sarah Rowe Hasty performed initial RNA isolation, purification and re-precipitation from 205 cell lines in Dr. Malak Kotb laboratory at VAMC. After initial RNA isolation, Ms. Nourtan Abdeltawab treated all samples for removal of contaminating DNA, along with further purification and re-precipitation of all samples. RNA samples that passed quality control were used to generate cRNA samples, those that didn't pass QC were re-extracted as we had duplicates of all cell lines lysates. RNA Extraction details: We used Qiagen RNeasy Mini purification of total RNA from tissues and cells spin protocol. RNA was isolated from 7.5 X 10<SUP>5</SUP> cells in duplicates. We froze cell lysates in RLT buffer and ß-mercaptoethanol at -80 ºC in 96 well plates until processed at a later time. We thawed samples, one 96 well plate at a time, and proceeded with RNA isolation steps and resuspended the pellets in RNase-free water. We then treated RNA to remove any DNA contamination using DNase digestion with RNase-free DNase kit (Qiagen) according to manufacturer protocol. RNA was finally purified by re-precipitation using ethanol precipitation using Purescript RNA purification kit (Gentra). Final purified RNA was resuspended in RNase-free water. RNA quality control: RNA samples were checked for RNA purity and integrity. RNA purity was evaluated using the 260/280 and 260/230 absorbance ratios. We used RNA samples with 260/280 ratio values ≥ 1.8 and 260/230 of ≥1.7. In cases were RNA samples did not meet these ratios, the RNA was purified by re-precipitation as above. RNA integrity was assessed using 1% RNA denaturing agrose gels. We required clear sharp bands of 18S and 28S rRNA for all samples compared to a control RNA sample to ensure intactness of rRNA.</P>
\ No newline at end of file diff --git a/general/datasets/Ut_ceph_rankinv0909/platform.rtf b/general/datasets/Ut_ceph_rankinv0909/platform.rtf new file mode 100644 index 0000000..a7a8769 --- /dev/null +++ b/general/datasets/Ut_ceph_rankinv0909/platform.rtf @@ -0,0 +1 @@ +<p><strong>Illumina HumanGW-6 v2.0 BeadChip: </strong>The Human-6 v2 beadchip simultaneously assays six samples, therefore, known as ‘array of arrays’. Each chip has ~1.8 million beads, beads have several hundred thousands copies of optimized 50-mer gene-specific probes. These probes cover more than 48,000 transcripts per sample, targeting genes and known alternative splice variants from the RefSeq database release 17 and UniGene build 188.</p>
diff --git a/general/datasets/Ut_ceph_rankinv0909/processing.rtf b/general/datasets/Ut_ceph_rankinv0909/processing.rtf new file mode 100644 index 0000000..d144cac --- /dev/null +++ b/general/datasets/Ut_ceph_rankinv0909/processing.rtf @@ -0,0 +1,3 @@ +<p><strong>About array data processing and analysis:</strong></p>
+
+<p>RNA samples (n = 180) were processed using a total of 30 Illumina HumanWG-6 BeadChips, each beadchip analyses six samples covering 48,000 transcripts per sample. All chips passed quality control and error checking. This data set was extracted and processed using the Bead Studio 3. We applied Rank-invariant normalization to all the samples and the resulting expression values along with gene ID were exported in GeneSpring format. Dr. Rita Kansal performed the normalization steps.</p>
diff --git a/general/datasets/Ut_ceph_rankinv0909/summary.rtf b/general/datasets/Ut_ceph_rankinv0909/summary.rtf new file mode 100644 index 0000000..4394cb5 --- /dev/null +++ b/general/datasets/Ut_ceph_rankinv0909/summary.rtf @@ -0,0 +1,7 @@ +<p>The Illumina Human Whole Genome 6 v2.0 Rank Invariant data for <a href="http://ccr.coriell.org/sections/Collections/nigms/CEPHFamilies.aspx?PgId=49&coll=GM">CEPH</a> lymphoblastoid cell lines obtained from the Coriell Institute for Medical Research. All cell lines were processed in Memphis in the UTHSC laboratory of Dr. Malak Kotb (2007-2009), by Dr. Rita G. Kasal, Nourtan Abdeltawab, and colleagues.</p>
+
+<p>Selection of CEPH families and members was done by <a href="http://dgsom.healthsciences.ucla.edu/research/institution/personnel?personnel_id=46538">Dr. Roel Ophoff</a> (Utrecht and UCLA).</p>
+
+<p>Array data were generated at microarray core facility in laboratory of Dr. Weikuan Gu at VA medical center, Memphis, TN.</p>
+
+<p>Analysis by <a href="http://www.biostatistics.vcu.edu/people/faculty/reimers.html">Mark Reimers</a>, <a href="http://www-math.cudenver.edu/~ssantori/">Stephanie Santorico</a>, and <a href="http://dgsom.healthsciences.ucla.edu/research/institution/personnel?personnel_id=46538">Roel Ophoff</a></p>
|