diff options
Diffstat (limited to 'general/datasets/INIA_Adrenal_RMA_M_0612')
6 files changed, 0 insertions, 794 deletions
diff --git a/general/datasets/INIA_Adrenal_RMA_M_0612/cases.rtf b/general/datasets/INIA_Adrenal_RMA_M_0612/cases.rtf deleted file mode 100644 index f0b204b..0000000 --- a/general/datasets/INIA_Adrenal_RMA_M_0612/cases.rtf +++ /dev/null @@ -1,771 +0,0 @@ -<p>Young adult mice raised in specific pathogen-free vivarium at UTHSC.<br />
-Table 1. Final strain correction by Khyobeni Mozhui on Mar 28, 2013.</p>
-
-<table align="left" border="1" cellpadding="0" cellspacing="0" style="width:60%">
- <tbody>
- <tr>
- <td>
- <table border="1" cellpadding="5" cellspacing="1" style="width:100%">
- <tbody>
- <tr>
- <td>Index</td>
- <td>Sample ID</td>
- <td>Strain</td>
- <td>Tissue</td>
- <td>Sex</td>
- </tr>
- <tr>
- <td>1</td>
- <td>R6947A</td>
- <td>BXD48</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>2</td>
- <td>R6948A</td>
- <td>BXD90</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>3</td>
- <td>R6949A</td>
- <td>BXD97</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>4</td>
- <td>R6950A</td>
- <td>BXD87</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>5</td>
- <td>R6952A</td>
- <td>BXD83</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>6</td>
- <td>R6953A</td>
- <td>BXD67</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>7</td>
- <td>R6954A</td>
- <td>BXD56</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>8</td>
- <td>R6955A</td>
- <td>BXD48</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>9</td>
- <td>R6956A</td>
- <td>BXD90</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>10</td>
- <td>R6957A</td>
- <td>BXD89</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>11</td>
- <td>R6958A</td>
- <td>BXD65</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>12</td>
- <td>R6959A</td>
- <td>BXD65</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>13</td>
- <td>R6960A</td>
- <td>BXD63</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>14</td>
- <td>R6961A</td>
- <td>BXD63</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>15</td>
- <td>R6963A</td>
- <td>BXD31</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>16</td>
- <td>R6964A</td>
- <td>BXD31</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>17</td>
- <td>R6965A</td>
- <td>BXD1</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>18</td>
- <td>R6966A</td>
- <td>BXD1</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>19</td>
- <td>R6967A</td>
- <td>BXD24</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>20</td>
- <td>R6968A</td>
- <td>BXD34</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>21</td>
- <td>R6969A</td>
- <td>BXD1</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>22</td>
- <td>R6971A</td>
- <td>BXD27</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>23</td>
- <td>R6972A</td>
- <td>BXD29</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>24</td>
- <td>R6973A</td>
- <td>BXD12</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>25</td>
- <td>R6974A</td>
- <td>BXD14</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>26</td>
- <td>R6975A</td>
- <td>BXD99</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>27</td>
- <td>R6976A</td>
- <td>BXD32</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>28</td>
- <td>R6977A</td>
- <td>BXD97</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>29</td>
- <td>R6978A</td>
- <td>BXD84</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>30</td>
- <td>R6979A</td>
- <td>BXD39</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>31</td>
- <td>R6980A</td>
- <td>BXD24</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>32</td>
- <td>R6981A</td>
- <td>BXD50</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>33</td>
- <td>R6982A</td>
- <td>BXD75</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>34</td>
- <td>R6983A</td>
- <td>BXD42</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>35</td>
- <td>R6984A</td>
- <td>BXD39</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>36</td>
- <td>R6985A</td>
- <td>BXD34</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>37</td>
- <td>R6986A</td>
- <td>BXD87</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>38</td>
- <td>R6987A</td>
- <td>BXD50</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>39</td>
- <td>R6989A</td>
- <td>BXD62</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>40</td>
- <td>R6990A</td>
- <td>BXD70</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>41</td>
- <td>R6991A</td>
- <td>BXD64</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>42</td>
- <td>R6992A</td>
- <td>BXD84</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>43</td>
- <td>R6993A</td>
- <td>BXD100</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>44</td>
- <td>R6994A</td>
- <td>BXD62</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>45</td>
- <td>R6996A</td>
- <td>BXD95</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>46</td>
- <td>R6998A</td>
- <td>BXD32</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>47</td>
- <td>R6999A</td>
- <td>BXD101</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>48</td>
- <td>R7000A</td>
- <td>BXD49</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>49</td>
- <td>R7002A</td>
- <td>BXD11</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>50</td>
- <td>R7003A</td>
- <td>BXD100</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>51</td>
- <td>R7004A</td>
- <td>BXD43</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>52</td>
- <td>R7005A</td>
- <td>BXD103</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>53</td>
- <td>R7006A</td>
- <td>BXD73</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>54</td>
- <td>R7008A</td>
- <td>BXD43</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>55</td>
- <td>R7009A</td>
- <td>BXD102</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>56</td>
- <td>R7010A</td>
- <td>BXD69</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>57</td>
- <td>R7011A</td>
- <td>BXD60</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>58</td>
- <td>R7012A</td>
- <td>BXD45</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>59</td>
- <td>R7013A</td>
- <td>BXD79</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>60</td>
- <td>R7014A</td>
- <td>BXD40</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>61</td>
- <td>R7015A</td>
- <td>BXD79</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>62</td>
- <td>R7016A</td>
- <td>BXD40</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>63</td>
- <td>R7017A</td>
- <td>BXD68</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>64</td>
- <td>R7018A</td>
- <td>BXD85</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>65</td>
- <td>R7019A</td>
- <td>BXD44</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>66</td>
- <td>R7020A</td>
- <td>BXD70</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>67</td>
- <td>R7021A</td>
- <td>BXD68</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>68</td>
- <td>R7023A</td>
- <td>BXD44</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>69</td>
- <td>R7024A</td>
- <td>BXD95</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>70</td>
- <td>R7025A</td>
- <td>BXD56</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>71</td>
- <td>R7032A</td>
- <td>BXD103</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>72</td>
- <td>R7034A</td>
- <td>BXD24</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>73</td>
- <td>R7035A</td>
- <td>BXD101</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>74</td>
- <td>R7036A</td>
- <td>BXD29</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>75</td>
- <td>R7037A</td>
- <td>BXD60</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>76</td>
- <td>R7038A</td>
- <td>BXD69</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>77</td>
- <td>R7039A</td>
- <td>BXD73</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>78</td>
- <td>R7040A</td>
- <td>BXD80</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>79</td>
- <td>R7041A</td>
- <td>BXD11</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>80</td>
- <td>R7042A</td>
- <td>BXD74</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>81</td>
- <td>R7043A</td>
- <td>BXD67</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>82</td>
- <td>R7044A</td>
- <td>BXD67</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>83</td>
- <td>R7046A</td>
- <td>C57BL/6J</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>84</td>
- <td>R7047A</td>
- <td>D2B6F1</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>85</td>
- <td>R7048A</td>
- <td>B6D2F1</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>86</td>
- <td>R7051A</td>
- <td>BXD80</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>87</td>
- <td>R7053A</td>
- <td>BXD102</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>88</td>
- <td>R7054A</td>
- <td>BXD49</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>89</td>
- <td>R7055A</td>
- <td>BXD77</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>90</td>
- <td>R7056A</td>
- <td>BXD77</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>91</td>
- <td>R7057A</td>
- <td>BXD66</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>92</td>
- <td>R7058A</td>
- <td>BXD66</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>93</td>
- <td>R7059A</td>
- <td>BXD45</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>94</td>
- <td>R7145A</td>
- <td>BXD67</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>95</td>
- <td>R7147A</td>
- <td>BXD85</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>96</td>
- <td>R7148A</td>
- <td>DBA/2J</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>97</td>
- <td>R7149A</td>
- <td>D2B6F1</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>98</td>
- <td>R7150A</td>
- <td>D2B6F1</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>99</td>
- <td>R7151A</td>
- <td>BXD27</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>100</td>
- <td>R7152A</td>
- <td>B6D2F1</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>101</td>
- <td>R7153A</td>
- <td>DBA/2J</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>102</td>
- <td>R7159A</td>
- <td>C57BL/6J</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>103</td>
- <td>R7161A</td>
- <td>C57BL/6J</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>104</td>
- <td>R7164A</td>
- <td>B6D2F1</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>105</td>
- <td>R7166A</td>
- <td>B6D2F1</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- <tr>
- <td>106</td>
- <td>R7167A</td>
- <td>DBA/2J</td>
- <td>Adrenal</td>
- <td>F</td>
- </tr>
- <tr>
- <td>107</td>
- <td>R7168A</td>
- <td>DBA/2J</td>
- <td>Adrenal</td>
- <td>M</td>
- </tr>
- </tbody>
- </table>
- </td>
- </tr>
- </tbody>
-</table>
diff --git a/general/datasets/INIA_Adrenal_RMA_M_0612/experiment-design.rtf b/general/datasets/INIA_Adrenal_RMA_M_0612/experiment-design.rtf deleted file mode 100644 index b069873..0000000 --- a/general/datasets/INIA_Adrenal_RMA_M_0612/experiment-design.rtf +++ /dev/null @@ -1,3 +0,0 @@ -<p>Normative expression in the adrenals (whole organ) of young adult mice. In general, a sex-balanced samples (one array from male cases, one array from female cases) for BXD and parental strains.</p>
-
-<p>Part of a systematic genetic analysis of the hypothalamus-pituitary-adrenal axis in the BXD family of strains.</p>
diff --git a/general/datasets/INIA_Adrenal_RMA_M_0612/platform.rtf b/general/datasets/INIA_Adrenal_RMA_M_0612/platform.rtf deleted file mode 100644 index 7057d48..0000000 --- a/general/datasets/INIA_Adrenal_RMA_M_0612/platform.rtf +++ /dev/null @@ -1 +0,0 @@ -<p>The GeneChip® Mouse Gene 1.0 ST Array is the latest product in the family of Affymetrix expression arrays offering whole-transcript coverage. Each of the 28,853 genes is represented on the array by approximately 27 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3'-based expression array designs. The small format of the array makes it a cost-effective expression profiling solution for new microarray users. Sense DNA targets are generated from as little as 100ng of total RNA. The Gene 1.0 ST Array is part of a complete solution for gene expression analysis that includes Whole Transcript (WT) Sense Target Labeling and Control Reagents, fluidics and scanning instrumentation and basic analysis software. The array contains the most up-to-date content of well-annotated genes, and data is analyzed using a simple workflow. The Gene 1.0 ST Array uses a subset of probes from the Mouse Exon 1.0 ST Array and covers only well-annotated content. Like the Exon 1.0 ST Array, "gene-level" analysis of multiple probes on different exons is summarized into an expression value representing all transcripts from the same gene.</p>
diff --git a/general/datasets/INIA_Adrenal_RMA_M_0612/processing.rtf b/general/datasets/INIA_Adrenal_RMA_M_0612/processing.rtf deleted file mode 100644 index 55aad2e..0000000 --- a/general/datasets/INIA_Adrenal_RMA_M_0612/processing.rtf +++ /dev/null @@ -1 +0,0 @@ -<p>Conventional Affymetrix gene level probe summarization (RMA) followed by log2 transformation and standard GeneNetwork variance stabilization (2z +8). The z scores are multiplied by 2 and we then add a value of 8 to all values. This eliminates negative values and results in a scale of expression for which 1 unit is roughly equivalent to a two fold absolute difference in mRNA concentration.</p>
diff --git a/general/datasets/INIA_Adrenal_RMA_M_0612/summary.rtf b/general/datasets/INIA_Adrenal_RMA_M_0612/summary.rtf deleted file mode 100644 index 9858a55..0000000 --- a/general/datasets/INIA_Adrenal_RMA_M_0612/summary.rtf +++ /dev/null @@ -1,17 +0,0 @@ -<p>Preliminary data WITH ERRORS of strain assignment as of July 20, 2012.</p>
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-<p>Original Assignment had 253 probe sets with LRS >46.</p>
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-<p>Corrections on Adrenal Data on July 25, 2012:<br />
-R6963A(BXD31).....it should be BXD34<br />
-R7018A(BXD85).....it should be BXD95<br />
-R7152A(C57BL/6J)...it should be B6D2F1<br />
-R7020A(BXD70).......it should be BXD65</p>
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-<p>229 probe sets with LRS >46 after the corrections above from S. Roy of July 25, July 26 AM.</p>
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-<p>More corrections from S. Roy (5 PM July 26)<br />
-R6965A(BXD42).........should be BXD2<br />
-R6973A(BXD12).........should be BXD8<br />
-R6985A(BXD34).........should be BXD8<br />
-R7151A(BXD99)..........should be BXD42</p>
diff --git a/general/datasets/INIA_Adrenal_RMA_M_0612/tissue.rtf b/general/datasets/INIA_Adrenal_RMA_M_0612/tissue.rtf deleted file mode 100644 index 54000a9..0000000 --- a/general/datasets/INIA_Adrenal_RMA_M_0612/tissue.rtf +++ /dev/null @@ -1 +0,0 @@ -<p>Whole adrenal gland. Dissections by Khyobeni Mozhui, Jesse Ingels, and Adrienne Adler at UTHSC.</p>
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