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-rw-r--r--general/datasets/ONCRetMoGene2_0413/acknowledgment.rtf1
-rw-r--r--general/datasets/ONCRetMoGene2_0413/cases.rtf1728
-rw-r--r--general/datasets/ONCRetMoGene2_0413/platform.rtf1
-rw-r--r--general/datasets/ONCRetMoGene2_0413/processing.rtf1
-rw-r--r--general/datasets/ONCRetMoGene2_0413/summary.rtf1
-rw-r--r--general/datasets/ONCRetMoGene2_0413/tissue.rtf1
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diff --git a/general/datasets/ONCRetMoGene2_0413/acknowledgment.rtf b/general/datasets/ONCRetMoGene2_0413/acknowledgment.rtf
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--- a/general/datasets/ONCRetMoGene2_0413/acknowledgment.rtf
+++ /dev/null
@@ -1 +0,0 @@
-<p>DoD funding (W81XWH-12-0255) Genetic Networks Activated by Blast Injury to the Eye (Eldon E. Geisert).</p>
diff --git a/general/datasets/ONCRetMoGene2_0413/cases.rtf b/general/datasets/ONCRetMoGene2_0413/cases.rtf
deleted file mode 100644
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-<p>Almost all animals are young adults between 60 and 90 days of age (Table 1, minimum age is 50 and maximum age is 134 days). We measured expression in conventional inbred strains, BXD recombinant inbred (RI) strains, and reciprocal F1s between C57BL/6J and DBA/2J. BXD strains: The first 32 of these strains are from the Taylor series of BXD strains generated at the Jackson Laboratory by Benjamin A. Taylor. BXD1 through BXD32 were started in the late 1970s, whereas BXD33 through 42 were started in the 1990s. In 2004, BXD24/TyJ developed a spontaneous mutation, rd16 which resulted in retinal degeneration and was renamed BXD24b/TyJ (BXD24 in this database). The strain, BXD24a, was cryo-recovered in 2004 from 1988 embryo stocks (F80) and does not exhibit retinal degeneration. In 2009, BXD24b was renamed BXD24/TyJ-Cep290rd16/J by JAX Labs to reflect the discovery of the genetic basis of the mutation. At the same time BXD24a was then referred to just as BXD24/TyJ by Jax Labs, but still called BXD24a in this dataset. The other 36 BXD strains (BXD43 and higher) were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams starting in 1997 using B6D2 generation 10 advanced intercross progeny. This modified breeding protocol doubles the number of recombinations per BXD strain and improves mapping resolution (Peirce et al. 2004). All of the Taylor series of BXD strains and many of the new BXD strains are available from the Jackson Laboratory. All of the new BXD strains (BXD43 and higher) are also available directly from Lu Lu and colleagues at the University of Tennessee Health Science Center in Memphis, TN, USA. BXD24/TyJ is now known as BXD24b/TyJ and has nearly complete retinal degeneration. BXD24a/TyJ, a 1988 F80 inbred stock that has been rederived from cryogenic storage, does not have retinal degeneration (stock number 005243) and is an ideal coisogenic control, but is not included in the HEI data set.</p>
-
-<blockquote>
-<table border="1" cellpadding="0" cellspacing="0" style="width:600px">
- <tbody>
- <tr>
- <td>
- <table align="left" border="1" cellpadding="5" cellspacing="1" class="sortable" style="width:600px">
- <tbody>
- <tr>
- <td>Index</td>
- <td>EIGC ID (LIMS ID)</td>
- <td>Strain</td>
- <td>Sex</td>
- <td>Age at harvest</td>
- <td>RIN Score</td>
- </tr>
- <tr>
- <td>1</td>
- <td>602</td>
- <td>BXD9</td>
- <td>F</td>
- <td>133</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>2</td>
- <td>603</td>
- <td>BXD9</td>
- <td>M</td>
- <td>100</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>3</td>
- <td>604</td>
- <td>BXD40</td>
- <td>F</td>
- <td>100</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>4</td>
- <td>605</td>
- <td>BXD40</td>
- <td>M</td>
- <td>100</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>5</td>
- <td>606</td>
- <td>BXD48</td>
- <td>F</td>
- <td>75</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>6</td>
- <td>607</td>
- <td>BXD48</td>
- <td>M</td>
- <td>75</td>
- <td>8.6</td>
- </tr>
- <tr>
- <td>7</td>
- <td>608</td>
- <td>BXD63</td>
- <td>F</td>
- <td>75</td>
- <td>9.2</td>
- </tr>
- <tr>
- <td>8</td>
- <td>609</td>
- <td>BXD63</td>
- <td>M</td>
- <td>61</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>9</td>
- <td>612</td>
- <td>BXD73</td>
- <td>M</td>
- <td>108</td>
- <td>10</td>
- </tr>
- <tr>
- <td>10</td>
- <td>614</td>
- <td>BXD87</td>
- <td>M</td>
- <td>85</td>
- <td>9.2</td>
- </tr>
- <tr>
- <td>11</td>
- <td>615</td>
- <td>BXD87</td>
- <td>F</td>
- <td>85</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>12</td>
- <td>616</td>
- <td>BXD69</td>
- <td>F</td>
- <td>76</td>
- <td>9.3</td>
- </tr>
- <tr>
- <td>13</td>
- <td>617</td>
- <td>BXD69</td>
- <td>M</td>
- <td>100</td>
- <td>10</td>
- </tr>
- <tr>
- <td>14</td>
- <td>618</td>
- <td>BXD51</td>
- <td>M</td>
- <td>82</td>
- <td>8.9</td>
- </tr>
- <tr>
- <td>15</td>
- <td>619</td>
- <td>BXD92 (BXD65b)</td>
- <td>M</td>
- <td>82</td>
- <td>8.8</td>
- </tr>
- <tr>
- <td>16</td>
- <td>620</td>
- <td>BXD92 (BXD65b)</td>
- <td>F</td>
- <td>82</td>
- <td>8.8</td>
- </tr>
- <tr>
- <td>17</td>
- <td>635</td>
- <td>BXD100</td>
- <td>M</td>
- <td>70</td>
- <td>9</td>
- </tr>
- <tr>
- <td>18</td>
- <td>636</td>
- <td>BXD100</td>
- <td>M</td>
- <td>70</td>
- <td>8.8</td>
- </tr>
- <tr>
- <td>19</td>
- <td>652</td>
- <td>BXD92 (BXD65b)</td>
- <td>F</td>
- <td>64</td>
- <td>9</td>
- </tr>
- <tr>
- <td>20</td>
- <td>653</td>
- <td>BXD87</td>
- <td>F</td>
- <td>67</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>21</td>
- <td>654</td>
- <td>BXD87</td>
- <td>M</td>
- <td>67</td>
- <td>8.9</td>
- </tr>
- <tr>
- <td>22</td>
- <td>655</td>
- <td>BXD63</td>
- <td>M</td>
- <td>71</td>
- <td>9</td>
- </tr>
- <tr>
- <td>23</td>
- <td>660</td>
- <td>BXD69</td>
- <td>M</td>
- <td>97</td>
- <td>10</td>
- </tr>
- <tr>
- <td>24</td>
- <td>687</td>
- <td>BXD6</td>
- <td>M</td>
- <td>85</td>
- <td>7.7</td>
- </tr>
- <tr>
- <td>25</td>
- <td>688</td>
- <td>BXD6</td>
- <td>M</td>
- <td>85</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>26</td>
- <td>690</td>
- <td>BXD12</td>
- <td>F</td>
- <td>83</td>
- <td>10</td>
- </tr>
- <tr>
- <td>27</td>
- <td>691</td>
- <td>BXD12</td>
- <td>F</td>
- <td>83</td>
- <td>10</td>
- </tr>
- <tr>
- <td>28</td>
- <td>692</td>
- <td>BXD12</td>
- <td>M</td>
- <td>83</td>
- <td>10</td>
- </tr>
- <tr>
- <td>29</td>
- <td>695</td>
- <td>BXD5</td>
- <td>F</td>
- <td>77</td>
- <td>10</td>
- </tr>
- <tr>
- <td>30</td>
- <td>696</td>
- <td>BXD5</td>
- <td>M</td>
- <td>77</td>
- <td>10</td>
- </tr>
- <tr>
- <td>31</td>
- <td>698</td>
- <td>BXD5</td>
- <td>F</td>
- <td>77</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>32</td>
- <td>699</td>
- <td>BXD5</td>
- <td>F</td>
- <td>77</td>
- <td>10</td>
- </tr>
- <tr>
- <td>33</td>
- <td>701</td>
- <td>BXD8</td>
- <td>M</td>
- <td>79</td>
- <td>10</td>
- </tr>
- <tr>
- <td>34</td>
- <td>702</td>
- <td>BXD8</td>
- <td>M</td>
- <td>79</td>
- <td>10</td>
- </tr>
- <tr>
- <td>35</td>
- <td>705</td>
- <td>BXD8</td>
- <td>F</td>
- <td>77</td>
- <td>9.2</td>
- </tr>
- <tr>
- <td>36</td>
- <td>707</td>
- <td>BXD15</td>
- <td>F</td>
- <td>77</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>37</td>
- <td>708</td>
- <td>BXD15</td>
- <td>F</td>
- <td>77</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>38</td>
- <td>710</td>
- <td>BXD15</td>
- <td>M</td>
- <td>77</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>39</td>
- <td>713</td>
- <td>BXD22</td>
- <td>F</td>
- <td>71</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>40</td>
- <td>714</td>
- <td>BXD22</td>
- <td>F</td>
- <td>71</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>41</td>
- <td>716</td>
- <td>BXD22</td>
- <td>M</td>
- <td>71</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>42</td>
- <td>717</td>
- <td>BXD22</td>
- <td>M</td>
- <td>71</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>43</td>
- <td>719</td>
- <td>BXD14</td>
- <td>F</td>
- <td>70</td>
- <td>9.2</td>
- </tr>
- <tr>
- <td>44</td>
- <td>722</td>
- <td>BXD14</td>
- <td>M</td>
- <td>70</td>
- <td>8.9</td>
- </tr>
- <tr>
- <td>45</td>
- <td>723</td>
- <td>BXD14</td>
- <td>M</td>
- <td>70</td>
- <td>9.2</td>
- </tr>
- <tr>
- <td>46</td>
- <td>725</td>
- <td>BXD18</td>
- <td>F</td>
- <td>70</td>
- <td>9</td>
- </tr>
- <tr>
- <td>47</td>
- <td>726</td>
- <td>BXD18</td>
- <td>F</td>
- <td>70</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>48</td>
- <td>728</td>
- <td>BXD18</td>
- <td>M</td>
- <td>70</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>49</td>
- <td>729</td>
- <td>BXD18</td>
- <td>M</td>
- <td>70</td>
- <td>9.2</td>
- </tr>
- <tr>
- <td>50</td>
- <td>731</td>
- <td>BXD19</td>
- <td>F</td>
- <td>66</td>
- <td>9.3</td>
- </tr>
- <tr>
- <td>51</td>
- <td>732</td>
- <td>BXD19</td>
- <td>F</td>
- <td>66</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>52</td>
- <td>734</td>
- <td>BXD19</td>
- <td>M</td>
- <td>66</td>
- <td>9.8</td>
- </tr>
- <tr>
- <td>53</td>
- <td>735</td>
- <td>BXD19</td>
- <td>M</td>
- <td>66</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>54</td>
- <td>737</td>
- <td>BXD21</td>
- <td>F</td>
- <td>71</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>55</td>
- <td>738</td>
- <td>BXD21</td>
- <td>F</td>
- <td>71</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>56</td>
- <td>740</td>
- <td>BXD21</td>
- <td>M</td>
- <td>71</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>57</td>
- <td>741</td>
- <td>BXD21</td>
- <td>M</td>
- <td>71</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>58</td>
- <td>743</td>
- <td>BXD2</td>
- <td>F</td>
- <td>70</td>
- <td>8.3</td>
- </tr>
- <tr>
- <td>59</td>
- <td>744</td>
- <td>BXD2</td>
- <td>F</td>
- <td>70</td>
- <td>8.6</td>
- </tr>
- <tr>
- <td>60</td>
- <td>746</td>
- <td>BXD2</td>
- <td>M</td>
- <td>70</td>
- <td>7.5</td>
- </tr>
- <tr>
- <td>61</td>
- <td>747</td>
- <td>BXD2</td>
- <td>M</td>
- <td>77</td>
- <td>8.6</td>
- </tr>
- <tr>
- <td>62</td>
- <td>768</td>
- <td>BXD48</td>
- <td>M</td>
- <td>121</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>63</td>
- <td>770</td>
- <td>BXD92 (BXD65b)</td>
- <td>M</td>
- <td>65</td>
- <td>10</td>
- </tr>
- <tr>
- <td>64</td>
- <td>771</td>
- <td>BXD101</td>
- <td>F</td>
- <td>85</td>
- <td>8.3</td>
- </tr>
- <tr>
- <td>65</td>
- <td>772</td>
- <td>BXD101</td>
- <td>F</td>
- <td>85</td>
- <td>9.3</td>
- </tr>
- <tr>
- <td>66</td>
- <td>773</td>
- <td>BXD101</td>
- <td>M</td>
- <td>86</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>67</td>
- <td>774</td>
- <td>BXD101</td>
- <td>M</td>
- <td>86</td>
- <td>9.8</td>
- </tr>
- <tr>
- <td>68</td>
- <td>775</td>
- <td>BXD102</td>
- <td>F</td>
- <td>66</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>69</td>
- <td>776</td>
- <td>BXD102</td>
- <td>F</td>
- <td>66</td>
- <td>10</td>
- </tr>
- <tr>
- <td>70</td>
- <td>777</td>
- <td>BXD102</td>
- <td>M</td>
- <td>84</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>71</td>
- <td>787</td>
- <td>BXD60</td>
- <td>M</td>
- <td>86</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>72</td>
- <td>788</td>
- <td>BXD60</td>
- <td>M</td>
- <td>86</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>73</td>
- <td>789</td>
- <td>BXD63</td>
- <td>F</td>
- <td>115</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>74</td>
- <td>790</td>
- <td>BXD100</td>
- <td>F</td>
- <td>72</td>
- <td>9.8</td>
- </tr>
- <tr>
- <td>75</td>
- <td>791</td>
- <td>BXD100</td>
- <td>F</td>
- <td>72</td>
- <td>10</td>
- </tr>
- <tr>
- <td>76</td>
- <td>818</td>
- <td>BXD51</td>
- <td>F</td>
- <td>77</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>77</td>
- <td>819</td>
- <td>BXD51</td>
- <td>F</td>
- <td>77</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>78</td>
- <td>820</td>
- <td>BXD51</td>
- <td>M</td>
- <td>72</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>79</td>
- <td>821</td>
- <td>BXD65</td>
- <td>M</td>
- <td>72</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>80</td>
- <td>822</td>
- <td>BXD65</td>
- <td>M</td>
- <td>65</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>81</td>
- <td>825</td>
- <td>BXD65</td>
- <td>F</td>
- <td>72</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>82</td>
- <td>827</td>
- <td>BXD86</td>
- <td>M</td>
- <td>69</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>83</td>
- <td>828</td>
- <td>BXD86</td>
- <td>M</td>
- <td>69</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>84</td>
- <td>829</td>
- <td>BXD90</td>
- <td>F</td>
- <td>69</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>85</td>
- <td>831</td>
- <td>BXD9</td>
- <td>M</td>
- <td>127</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>86</td>
- <td>832</td>
- <td>BXD39</td>
- <td>F</td>
- <td>99</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>87</td>
- <td>833</td>
- <td>BXD39</td>
- <td>F</td>
- <td>107</td>
- <td>9.3</td>
- </tr>
- <tr>
- <td>88</td>
- <td>834</td>
- <td>BXD60</td>
- <td>F</td>
- <td>107</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>89</td>
- <td>836</td>
- <td>BXD84</td>
- <td>M</td>
- <td>103</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>90</td>
- <td>846</td>
- <td>BXD39</td>
- <td>M</td>
- <td>63</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>91</td>
- <td>847</td>
- <td>BXD39</td>
- <td>M</td>
- <td>63</td>
- <td>9.8</td>
- </tr>
- <tr>
- <td>92</td>
- <td>849</td>
- <td>BXD20</td>
- <td>F</td>
- <td>70</td>
- <td>10</td>
- </tr>
- <tr>
- <td>93</td>
- <td>850</td>
- <td>BXD20</td>
- <td>M</td>
- <td>70</td>
- <td>10</td>
- </tr>
- <tr>
- <td>94</td>
- <td>851</td>
- <td>BXD20</td>
- <td>*</td>
- <td>70</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>95</td>
- <td>855</td>
- <td>DBA/2J</td>
- <td>F</td>
- <td>78</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>96</td>
- <td>856</td>
- <td>DBA/2J</td>
- <td>F</td>
- <td>78</td>
- <td>10</td>
- </tr>
- <tr>
- <td>97</td>
- <td>857</td>
- <td>DBA/2J</td>
- <td>M</td>
- <td>78</td>
- <td>10</td>
- </tr>
- <tr>
- <td>98</td>
- <td>858</td>
- <td>DBA/2J</td>
- <td>M</td>
- <td>78</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>99</td>
- <td>859</td>
- <td>C57BL/6J</td>
- <td>F</td>
- <td>78</td>
- <td>10</td>
- </tr>
- <tr>
- <td>100</td>
- <td>860</td>
- <td>C57BL/6J</td>
- <td>F</td>
- <td>78</td>
- <td>10</td>
- </tr>
- <tr>
- <td>101</td>
- <td>861</td>
- <td>C57BL/6J</td>
- <td>M</td>
- <td>78</td>
- <td>10</td>
- </tr>
- <tr>
- <td>102</td>
- <td>862</td>
- <td>C57BL/6J</td>
- <td>M</td>
- <td>78</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>103</td>
- <td>EGE10907-0172_890_20844</td>
- <td>BXD28</td>
- <td>M</td>
- <td>75</td>
- <td>10</td>
- </tr>
- <tr>
- <td>104</td>
- <td>EGE10907-0173_891_20845</td>
- <td>BXD28</td>
- <td>M</td>
- <td>75</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>105</td>
- <td>EGE10907-0174_892_20846</td>
- <td>BXD28</td>
- <td>F</td>
- <td>75</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>106</td>
- <td>EGE10907-0176_895_20848</td>
- <td>BXD33</td>
- <td>M</td>
- <td>75</td>
- <td>9.88</td>
- </tr>
- <tr>
- <td>107</td>
- <td>EGE10907-0177_896_20849</td>
- <td>BXD33</td>
- <td>F</td>
- <td>75</td>
- <td>10</td>
- </tr>
- <tr>
- <td>108</td>
- <td>EGE10907-0178_897_20850</td>
- <td>BXD33</td>
- <td>F</td>
- <td>75</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>109</td>
- <td>EGE10907-0179_898_20851</td>
- <td>BXD36</td>
- <td>M</td>
- <td>75</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>110</td>
- <td>EGE10907-0180_899_20852</td>
- <td>BXD36</td>
- <td>F</td>
- <td>75</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>111</td>
- <td>EGE10907-0181_900_20853</td>
- <td>BXD36</td>
- <td>F</td>
- <td>75</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>112</td>
- <td>EGE10907-0182_910_20854</td>
- <td>BXD27</td>
- <td>M</td>
- <td>70</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>113</td>
- <td>EGE10907-0183_990_20855</td>
- <td>BXD9</td>
- <td>F</td>
- <td>98</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>114</td>
- <td>EGE10907-0184_991_20856</td>
- <td>BXD16</td>
- <td>F</td>
- <td>113</td>
- <td>10</td>
- </tr>
- <tr>
- <td>115</td>
- <td>EGE10907-0185_992_20857</td>
- <td>BXD16</td>
- <td>M</td>
- <td>113</td>
- <td>9</td>
- </tr>
- <tr>
- <td>116</td>
- <td>EGE10907-0186_993_20858</td>
- <td>BXD27</td>
- <td>F</td>
- <td>96</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>117</td>
- <td>EGE10907-0187_994_20859</td>
- <td>BXD27</td>
- <td>F</td>
- <td>96</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>118</td>
- <td>EGE10907-0188_996_20860</td>
- <td>BXD48</td>
- <td>F</td>
- <td>98</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>119</td>
- <td>EGE10907-0189_997_20861</td>
- <td>BXD73</td>
- <td>M</td>
- <td>106</td>
- <td>10</td>
- </tr>
- <tr>
- <td>120</td>
- <td>EGE10907-0190_999_20862</td>
- <td>BXD11</td>
- <td>F</td>
- <td>121</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>121</td>
- <td>EGE10907-0191_100_20863</td>
- <td>BXD11</td>
- <td>F</td>
- <td>121</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>122</td>
- <td>EGE10907-0192_1010_21276</td>
- <td>BXD13</td>
- <td>M</td>
- <td>69</td>
- <td>9.8</td>
- </tr>
- <tr>
- <td>123</td>
- <td>EGE10907-0193_1011_21277</td>
- <td>BXD13</td>
- <td>M</td>
- <td>69</td>
- <td>9.8</td>
- </tr>
- <tr>
- <td>124</td>
- <td>EGE10907-0194_1012_21278</td>
- <td>BXD16</td>
- <td>F</td>
- <td>65</td>
- <td>10</td>
- </tr>
- <tr>
- <td>125</td>
- <td>EGE10907-0195_1015_21279</td>
- <td>BXD16</td>
- <td>M</td>
- <td>65</td>
- <td>10</td>
- </tr>
- <tr>
- <td>126</td>
- <td>EGE10907-0196_1019_21280</td>
- <td>BXD33</td>
- <td>M</td>
- <td>75</td>
- <td>10</td>
- </tr>
- <tr>
- <td>127</td>
- <td>EGE10907-0197_1020_21281</td>
- <td>BXD36</td>
- <td>M</td>
- <td>78</td>
- <td>10</td>
- </tr>
- <tr>
- <td>128</td>
- <td>EGE10907-0198_1021_21282</td>
- <td>BXD38</td>
- <td>F</td>
- <td>70</td>
- <td>9.8</td>
- </tr>
- <tr>
- <td>129</td>
- <td>EGE10907-0199_1022_21283</td>
- <td>BXD38</td>
- <td>F</td>
- <td>70</td>
- <td>10</td>
- </tr>
- <tr>
- <td>130</td>
- <td>EGE10907-0200_1023_21284</td>
- <td>BXD38</td>
- <td>M</td>
- <td>70</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>131</td>
- <td>EGE10907-0201_1047_21285</td>
- <td>BXD11</td>
- <td>M</td>
- <td>65</td>
- <td>10</td>
- </tr>
- <tr>
- <td>132</td>
- <td>EGE10907-0202_1048_21286</td>
- <td>BXD11</td>
- <td>M</td>
- <td>65</td>
- <td>10</td>
- </tr>
- <tr>
- <td>133</td>
- <td>EGE10907-0203_1049_21287</td>
- <td>BXD38</td>
- <td>M</td>
- <td>77</td>
- <td>10</td>
- </tr>
- <tr>
- <td>134</td>
- <td>EGE10907-0204_1050_21288</td>
- <td>BXD73</td>
- <td>F</td>
- <td>70</td>
- <td>10</td>
- </tr>
- <tr>
- <td>135</td>
- <td>EGE10907-0205_1051_21289</td>
- <td>BXD73</td>
- <td>F</td>
- <td>70</td>
- <td>10</td>
- </tr>
- <tr>
- <td>136</td>
- <td>EGE10907-0206_1052_21290</td>
- <td>BXD86</td>
- <td>F</td>
- <td>69</td>
- <td>10</td>
- </tr>
- <tr>
- <td>137</td>
- <td>EGE10907-0207_1053_21291</td>
- <td>BXD86</td>
- <td>F</td>
- <td>69</td>
- <td>10</td>
- </tr>
- <tr>
- <td>138</td>
- <td>EGE10907-0208_1054_21292</td>
- <td>BXD90</td>
- <td>F</td>
- <td>71</td>
- <td>10</td>
- </tr>
- <tr>
- <td>139</td>
- <td>EGE10907-0209_1055_21293</td>
- <td>BXD90</td>
- <td>M</td>
- <td>71</td>
- <td>10</td>
- </tr>
- <tr>
- <td>140</td>
- <td>EGE10907-0210_1056_21294</td>
- <td>BXD90</td>
- <td>M</td>
- <td>71</td>
- <td>10</td>
- </tr>
- <tr>
- <td>141</td>
- <td>EGE10907-0211_1148_21295</td>
- <td>BXD31</td>
- <td>F</td>
- <td>90</td>
- <td>10</td>
- </tr>
- <tr>
- <td>142</td>
- <td>EGE10907-0212_1149_21296</td>
- <td>BXD31</td>
- <td>F</td>
- <td>90</td>
- <td>10</td>
- </tr>
- <tr>
- <td>143</td>
- <td>EGE10907-0213_1150_21297</td>
- <td>BXD31</td>
- <td>M</td>
- <td>90</td>
- <td>10</td>
- </tr>
- <tr>
- <td>144</td>
- <td>EGE10907-0214_1151_21298</td>
- <td>BXD31</td>
- <td>M</td>
- <td>90</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>145</td>
- <td>EGE10907-0215_1152_21299</td>
- <td>BXD42</td>
- <td>F</td>
- <td>83</td>
- <td>10</td>
- </tr>
- <tr>
- <td>146</td>
- <td>EGE10907-0216_21429</td>
- <td>BXD42</td>
- <td>F</td>
- <td>83</td>
- <td>10</td>
- </tr>
- <tr>
- <td>147</td>
- <td>EGE10907-0217_21430</td>
- <td>BXD42</td>
- <td>M</td>
- <td>83</td>
- <td>10</td>
- </tr>
- <tr>
- <td>148</td>
- <td>EGE10907-0218_21431</td>
- <td>BXD42</td>
- <td>M</td>
- <td>83</td>
- <td>9.3</td>
- </tr>
- <tr>
- <td>149</td>
- <td>EGE10907-0219_21432</td>
- <td>BXD50</td>
- <td>F</td>
- <td>92</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>150</td>
- <td>EGE10907-0220_21433</td>
- <td>BXD50</td>
- <td>F</td>
- <td>92</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>151</td>
- <td>EGE10907-0221_21434</td>
- <td>BXD50</td>
- <td>F</td>
- <td>92</td>
- <td>10</td>
- </tr>
- <tr>
- <td>152</td>
- <td>EGE10907-0222_21435</td>
- <td>BXD1</td>
- <td>M</td>
- <td>73</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>153</td>
- <td>EGE10907-0223_21436</td>
- <td>BXD13</td>
- <td>F</td>
- <td>71</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>154</td>
- <td>EGE10907-0224_21437</td>
- <td>BXD1</td>
- <td>M</td>
- <td>71</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>155</td>
- <td>EGE10907-0225_21438</td>
- <td>BXD13</td>
- <td>F</td>
- <td>71</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>156</td>
- <td>EGE10907-0226_21439</td>
- <td>BXD43</td>
- <td>F</td>
- <td>85</td>
- <td>10</td>
- </tr>
- <tr>
- <td>157</td>
- <td>EGE10907-0227_21452</td>
- <td>BXD43</td>
- <td>F</td>
- <td>85</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>158</td>
- <td>EGE10907-0229_21442</td>
- <td>BXD43</td>
- <td>M</td>
- <td>85</td>
- <td>8.2</td>
- </tr>
- <tr>
- <td>159</td>
- <td>EGE10907-0230_21443</td>
- <td>BXD50</td>
- <td>M</td>
- <td>69</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>160</td>
- <td>EGE10907-0231_21444</td>
- <td>BXD1</td>
- <td>F</td>
- <td>68</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>161</td>
- <td>EGE10907-0232_21445</td>
- <td>BXD1</td>
- <td>F</td>
- <td>68</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>162</td>
- <td>EGE10907-0233_21446</td>
- <td>BXD29</td>
- <td>M</td>
- <td>65</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>163</td>
- <td>EGE10907-0234_21447</td>
- <td>BXD29</td>
- <td>M</td>
- <td>65</td>
- <td>10</td>
- </tr>
- <tr>
- <td>164</td>
- <td>EGE10907-0235_21448</td>
- <td>BXD75</td>
- <td>F</td>
- <td>68</td>
- <td>10</td>
- </tr>
- <tr>
- <td>165</td>
- <td>EGE10907-0236_21449</td>
- <td>BXD75</td>
- <td>M</td>
- <td>68</td>
- <td>10</td>
- </tr>
- <tr>
- <td>166</td>
- <td>EGE10907-0237_21450</td>
- <td>BXD96</td>
- <td>F</td>
- <td>67</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>167</td>
- <td>EGE10907-0238_21931</td>
- <td>BXD99</td>
- <td>M</td>
- <td>71</td>
- <td>7.9</td>
- </tr>
- <tr>
- <td>168</td>
- <td>EGE10907-0239_21932</td>
- <td>BXD99</td>
- <td>M</td>
- <td>71</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>169</td>
- <td>EGE10907-0240_21933</td>
- <td>BXD67</td>
- <td>F</td>
- <td>68</td>
- <td>8.8</td>
- </tr>
- <tr>
- <td>170</td>
- <td>EGE10907-0241_21934</td>
- <td>BXD67</td>
- <td>F</td>
- <td>68</td>
- <td>8.5</td>
- </tr>
- <tr>
- <td>171</td>
- <td>EGE10907-0242_21935</td>
- <td>BXD67</td>
- <td>M</td>
- <td>68</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>172</td>
- <td>EGE10907-0243_21936</td>
- <td>BXD67</td>
- <td>M</td>
- <td>68</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>173</td>
- <td>EGE10907-0244_21937</td>
- <td>BXD6</td>
- <td>F</td>
- <td>68</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>174</td>
- <td>EGE10907-0245_21938</td>
- <td>BXD12</td>
- <td>M</td>
- <td>82</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>175</td>
- <td>EGE10907-0246_21939</td>
- <td>BXD60</td>
- <td>F</td>
- <td>72</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>176</td>
- <td>EGE10907-0247_21940</td>
- <td>BXD65</td>
- <td>F</td>
- <td>75</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>177</td>
- <td>EGE10907-0248_21941</td>
- <td>BXD75</td>
- <td>F</td>
- <td>69</td>
- <td>8.8</td>
- </tr>
- <tr>
- <td>178</td>
- <td>EGE10907-0249_21942_(MoGene-2_0-st)</td>
- <td>BXD75</td>
- <td>M</td>
- <td>69</td>
- <td>9.2</td>
- </tr>
- <tr>
- <td>179</td>
- <td>EGE10907-0250_21943</td>
- <td>BXD8</td>
- <td>F</td>
- <td>97</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>180</td>
- <td>EGE10907-0251_21944</td>
- <td>BXD85</td>
- <td>F</td>
- <td>79</td>
- <td>8.6</td>
- </tr>
- <tr>
- <td>181</td>
- <td>EGE10907-0252_21945</td>
- <td>BXD85</td>
- <td>M</td>
- <td>79</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>182</td>
- <td>EGE10907-0253_21946</td>
- <td>BXD85</td>
- <td>M</td>
- <td>79</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>183</td>
- <td>EGE10907-0254_21947</td>
- <td>BXD102</td>
- <td>M</td>
- <td>94</td>
- <td>8.6</td>
- </tr>
- <tr>
- <td>184</td>
- <td>EGE10907-0255_21948</td>
- <td>BXD99</td>
- <td>F</td>
- <td>83</td>
- <td>9</td>
- </tr>
- <tr>
- <td>185</td>
- <td>EGE10907-0256_21949</td>
- <td>BXD69</td>
- <td>F</td>
- <td>68</td>
- <td>9</td>
- </tr>
- <tr>
- <td>186</td>
- <td>EGE10907-0257_21950</td>
- <td>BXD84</td>
- <td>F</td>
- <td>74</td>
- <td>9.5</td>
- </tr>
- <tr>
- <td>187</td>
- <td>EGE10907-0258_21951</td>
- <td>BXD84</td>
- <td>F</td>
- <td>74</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>188</td>
- <td>EGE10907-0259_21952</td>
- <td>BXD84</td>
- <td>M</td>
- <td>74</td>
- <td>8.6</td>
- </tr>
- <tr>
- <td>189</td>
- <td>EGE10907-0260_21451</td>
- <td>BXD96</td>
- <td>M</td>
- <td>67</td>
- <td>9.2</td>
- </tr>
- <tr>
- <td>190</td>
- <td>EGE10907-0261_21452</td>
- <td>BXD99</td>
- <td>F</td>
- <td>71</td>
- <td>8.9</td>
- </tr>
- <tr>
- <td>191</td>
- <td>EGE10907-0262_21931</td>
- <td>BXD6</td>
- <td>F</td>
- <td>66</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>192</td>
- <td>EGE10907-0263_21932</td>
- <td>BXD14</td>
- <td>F</td>
- <td>69</td>
- <td>8.5</td>
- </tr>
- <tr>
- <td>193</td>
- <td>EGE10907-0264_21933</td>
- <td>BXD34</td>
- <td>M</td>
- <td>79</td>
- <td>9.1</td>
- </tr>
- <tr>
- <td>194</td>
- <td>EGE10907-0265_21934</td>
- <td>BXD34</td>
- <td>M</td>
- <td>79</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>195</td>
- <td>EGE10907-0266_21935</td>
- <td>BXD40</td>
- <td>F</td>
- <td>75</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>196</td>
- <td>EGE10907-0267_21936</td>
- <td>BXD40</td>
- <td>M</td>
- <td>78</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>197</td>
- <td>EGE10907-0268_21937</td>
- <td>BXD56</td>
- <td>F</td>
- <td>72</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>198</td>
- <td>EGE10907-0269_21938</td>
- <td>BXD56</td>
- <td>F</td>
- <td>72</td>
- <td>9.7</td>
- </tr>
- <tr>
- <td>199</td>
- <td>EGE10907-0270_21939</td>
- <td>BXD56</td>
- <td>M</td>
- <td>72</td>
- <td>9.6</td>
- </tr>
- <tr>
- <td>200</td>
- <td>EGE10907-0271_21940</td>
- <td>BXD56</td>
- <td>M</td>
- <td>72</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>201</td>
- <td>EGE10907-0272_21941</td>
- <td>BXD71</td>
- <td>F</td>
- <td>72</td>
- <td>9.9</td>
- </tr>
- <tr>
- <td>202</td>
- <td>EGE10907-0273_21942</td>
- <td>BXD71</td>
- <td>F</td>
- <td>75</td>
- <td>9.4</td>
- </tr>
- <tr>
- <td>203</td>
- <td>EGE10907-0274_21943</td>
- <td>BXD71</td>
- <td>M</td>
- <td>75</td>
- <td>10</td>
- </tr>
- <tr>
- <td>204</td>
- <td>EGE10907-0275_21944</td>
- <td>BXD71</td>
- <td>M</td>
- <td>75</td>
- <td>10</td>
- </tr>
- <tr>
- <td>205</td>
- <td>EGE10907-0276_21945</td>
- <td>BXD27</td>
- <td>M</td>
- <td>65</td>
- <td>10</td>
- </tr>
- <tr>
- <td>206</td>
- <td>EGE10907-0277_21946</td>
- <td>BXD15</td>
- <td>M</td>
- <td>65</td>
- <td>10</td>
- </tr>
- <tr>
- <td>207</td>
- <td>EGE10907-0278_21947</td>
- <td>BXD20</td>
- <td>F</td>
- <td>125</td>
- <td>10</td>
- </tr>
- <tr>
- <td>208</td>
- <td>EGE10907-0279_21948</td>
- <td>BXD29</td>
- <td>F</td>
- <td>77</td>
- <td>10</td>
- </tr>
- <tr>
- <td>209</td>
- <td>EGE10907-0280_21949</td>
- <td>BXD29</td>
- <td>F</td>
- <td>77</td>
- <td>10</td>
- </tr>
- <tr>
- <td>210</td>
- <td>EGE10907-0281_21950</td>
- <td>BXD34</td>
- <td>F</td>
- <td>74</td>
- <td>10</td>
- </tr>
- <tr>
- <td>211</td>
- <td>EGE10907-0282_21951</td>
- <td>BXD34</td>
- <td>F</td>
- <td>74</td>
- <td>10</td>
- </tr>
- <tr>
- <td>212</td>
- <td>EGE10907-0283_21952</td>
- <td>BXD85</td>
- <td>F</td>
- <td>87</td>
- <td>10</td>
- </tr>
- <tr>
- <td>213</td>
- <td>EGE10907-0284_21451</td>
- <td>BXD43</td>
- <td>M</td>
- <td>75</td>
- <td>9.8</td>
- </tr>
- </tbody>
- </table>
- </td>
- </tr>
- </tbody>
-</table>
-</blockquote>
diff --git a/general/datasets/ONCRetMoGene2_0413/platform.rtf b/general/datasets/ONCRetMoGene2_0413/platform.rtf
deleted file mode 100644
index 19fc38c..0000000
--- a/general/datasets/ONCRetMoGene2_0413/platform.rtf
+++ /dev/null
@@ -1 +0,0 @@
-<p>The Affymetrics GeneChip&amp;reg; Mouse Gene 2.0 ST microarrays. This relatively recent microarray was specifically designed to represent the whole-transcriptome. It includes probes to measure mRNA, long intergenic non-coding RNAs and microRNAs. Researchers have identified many transcripts in the mouse genome that do not have protein coding potential. Most of these non-coding RNAs have little functional annotation. Nonetheless, there is considerable evidence that these non-coding RNAs play important roles in development of the retina and the progression of disease. The coverage in the new ST 2.0 array includes over 28,000 coding transcripts and over 7,000 non-coding transcripts. There are also probes on the array covering 590 microRNAs.</p>
diff --git a/general/datasets/ONCRetMoGene2_0413/processing.rtf b/general/datasets/ONCRetMoGene2_0413/processing.rtf
deleted file mode 100644
index a7b767e..0000000
--- a/general/datasets/ONCRetMoGene2_0413/processing.rtf
+++ /dev/null
@@ -1 +0,0 @@
-<p>Replication, sex, and sample balance: Our goal was to obtain data for independent biological sample pools from both sexes for most lines of mice. The four batches of arrays included in this final data set, collectively represent a reasonably well-balanced sample of males and females, in general without within-strain-by-sex replication.</p>
diff --git a/general/datasets/ONCRetMoGene2_0413/summary.rtf b/general/datasets/ONCRetMoGene2_0413/summary.rtf
deleted file mode 100644
index 96a87e5..0000000
--- a/general/datasets/ONCRetMoGene2_0413/summary.rtf
+++ /dev/null
@@ -1 +0,0 @@
-<p>The DoD dataset was constructed using the Affymetrics GeneChip&reg; Mouse Gene 2.0 ST microarrays. This relatively recent microarray was specifically designed to represent the whole-transcriptome. It includes probes to measure mRNA, long intergenic non-coding RNAs and microRNAs. Researchers have identified many transcripts in the mouse genome that do not have protein coding potential. Most of these non-coding RNAs have little functional annotation. There is considerable evidence that these non-coding RNAs play important roles in development of the retina and the progression of disease. The coverage in the new ST 2.0 array includes over 28,000 coding transcripts and over 7,000 non-coding transcripts. There are also probes on the array covering 590 microRNAs. This is RMA expression data that has been normalized using what we call a 2z+8 scale, but without special correction for batch effects. The data for each strains were computed as the mean of four samples per strain. Expression values on a log2 scale range from 3.77 to 14.62, a nominal range of approximately 3600-fold. After taking the log2 of the original non-logged expression estimates, we convert data within an array to a z score. We then multiply the z score by 2. Finally, we add 8 units to ensure that no values are negative. The result is a scale with a mean of 8 units and a standard deviation of 2 units. A two-fold difference in expression is equivalent roughly to 1 unit on this scale.</p>
diff --git a/general/datasets/ONCRetMoGene2_0413/tissue.rtf b/general/datasets/ONCRetMoGene2_0413/tissue.rtf
deleted file mode 100644
index 056d7eb..0000000
--- a/general/datasets/ONCRetMoGene2_0413/tissue.rtf
+++ /dev/null
@@ -1 +0,0 @@
-<p>Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Retinas were removed immediately and placed in RiboLock (RiboLock: Thermo Scientific RiboLock RNase #EO0381 40U/&amp;micro;l 2500U) at room temperature. Individual retinas from the mouse were stored in each tube. RNA was isolated using a Qiacube with the resultant RIN scores ranging from 8.5 to 10.0.</p>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-14 22:13:06 +0000