diff options
| author | Bonface | 2024-02-13 23:52:26 -0600 |
|---|---|---|
| committer | Munyoki Kilyungi | 2024-08-09 13:30:43 +0300 |
| commit | b2feda451ccfbeaed02dce9088d6dd228cf15861 (patch) | |
| tree | 3dd2883524985114070a7770cd2e9f9bd7eb1848 /general/datasets/Inia_pg_rma_ex_0612 | |
| parent | d029d5d7f8ead1f1de8d318045004a4a6f68f5fb (diff) | |
| download | gn-docs-b2feda451ccfbeaed02dce9088d6dd228cf15861.tar.gz | |
Update dataset RTF Files.
Diffstat (limited to 'general/datasets/Inia_pg_rma_ex_0612')
9 files changed, 859 insertions, 0 deletions
diff --git a/general/datasets/Inia_pg_rma_ex_0612/acknowledgment.rtf b/general/datasets/Inia_pg_rma_ex_0612/acknowledgment.rtf new file mode 100644 index 0000000..f8bf764 --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/acknowledgment.rtf @@ -0,0 +1 @@ +<p>NIAAA U01 support to RWW.</p>
diff --git a/general/datasets/Inia_pg_rma_ex_0612/cases.rtf b/general/datasets/Inia_pg_rma_ex_0612/cases.rtf new file mode 100644 index 0000000..faf8ab0 --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/cases.rtf @@ -0,0 +1,840 @@ +<p>Young adult mice raised in specific pathogen-free vivarium at UTHSC.</p>
+
+<p>ERROR CHECKING by Mozhui, Centeno and Roy: The changes have been applied in GeneNetwork (GN389 - Pituitary) as follow:</p>
+
+<p>SampleId - New Strain Assignment<br />
+R7087P (was BXD101) = BXD100<br />
+R7138P_RW170 (was BXD85) = BXD95<br />
+R7156P (was C57BL/6J) = B6D2F1<br />
+R7141P = BXD65</p>
+
+<p> </p>
+
+<table align="left" border="1" cellpadding="0" cellspacing="0" style="width:50%">
+ <tbody>
+ <tr>
+ <td>
+ <table border="1" cellpadding="5" cellspacing="1" class="sortable" style="width:100%">
+ <tbody>
+ <tr>
+ <td>Index</td>
+ <td>Sample ID</td>
+ <td>Strain</td>
+ <td>Tissue</td>
+ <td>Age</td>
+ <td>Sex</td>
+ </tr>
+ <tr>
+ <td>1</td>
+ <td>R7128P</td>
+ <td>B6D2F1</td>
+ <td>Pituitary</td>
+ <td>69</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>2</td>
+ <td>R7156P</td>
+ <td>B6D2F1</td>
+ <td>Pituitary</td>
+ <td>92</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>3</td>
+ <td>R7129P</td>
+ <td>B6D2F1</td>
+ <td>Pituitary</td>
+ <td>69</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>4</td>
+ <td>R7134P</td>
+ <td>D2B6F1</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>5</td>
+ <td>R7133P</td>
+ <td>D2B6F1</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>6</td>
+ <td>R7160P</td>
+ <td>C57BL/6J</td>
+ <td>Pituitary</td>
+ <td>92</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>7</td>
+ <td>R7127P</td>
+ <td>C57BL/6J</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>8</td>
+ <td>R7126P</td>
+ <td>DBA/2J</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>9</td>
+ <td>R7157P</td>
+ <td>DBA/2J</td>
+ <td>Pituitary</td>
+ <td>75</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>10</td>
+ <td>R7125P</td>
+ <td>DBA/2J</td>
+ <td>Pituitary</td>
+ <td>68</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>11</td>
+ <td>R7155P</td>
+ <td>DBA/2J</td>
+ <td>Pituitary</td>
+ <td>75</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>12</td>
+ <td>R7058P</td>
+ <td>BXD1</td>
+ <td>Pituitary</td>
+ <td>72</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>13</td>
+ <td>R7063P</td>
+ <td>BXD1</td>
+ <td>Pituitary</td>
+ <td>86</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>14</td>
+ <td>R7079P</td>
+ <td>BXD11</td>
+ <td>Pituitary</td>
+ <td>87</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>15</td>
+ <td>R7069P</td>
+ <td>BXD11</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>16</td>
+ <td>R7051P</td>
+ <td>BXD12</td>
+ <td>Pituitary</td>
+ <td>78</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>17</td>
+ <td>R7061P</td>
+ <td>BXD12</td>
+ <td>Pituitary</td>
+ <td>78</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>18</td>
+ <td>R7064P</td>
+ <td>BXD14</td>
+ <td>Pituitary</td>
+ <td>81</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>19</td>
+ <td>R7066P</td>
+ <td>BXD14</td>
+ <td>Pituitary</td>
+ <td>81</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>20</td>
+ <td>R7052P</td>
+ <td>BXD24</td>
+ <td>Pituitary</td>
+ <td>86</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>21</td>
+ <td>R7076P</td>
+ <td>BXD27</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>22</td>
+ <td>R7071P</td>
+ <td>BXD27</td>
+ <td>Pituitary</td>
+ <td>73</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>23</td>
+ <td>R7059P</td>
+ <td>BXD29</td>
+ <td>Pituitary</td>
+ <td>72</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>24</td>
+ <td>R7060P</td>
+ <td>BXD29</td>
+ <td>Pituitary</td>
+ <td>72</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>25</td>
+ <td>R7055P</td>
+ <td>BXD31</td>
+ <td>Pituitary</td>
+ <td>74</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>26</td>
+ <td>R7062P</td>
+ <td>BXD31</td>
+ <td>Pituitary</td>
+ <td>74</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>27</td>
+ <td>R7143P</td>
+ <td>BXD32</td>
+ <td>Pituitary</td>
+ <td>81</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>28</td>
+ <td>R7135P</td>
+ <td>BXD32</td>
+ <td>Pituitary</td>
+ <td>81</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>29</td>
+ <td>R7119P</td>
+ <td>BXD34</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>30</td>
+ <td>R7054P</td>
+ <td>BXD34</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>31</td>
+ <td>R7049P</td>
+ <td>BXD39</td>
+ <td>Pituitary</td>
+ <td>79</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>32</td>
+ <td>R7065P</td>
+ <td>BXD39</td>
+ <td>Pituitary</td>
+ <td>79</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>33</td>
+ <td>R7130P</td>
+ <td>BXD40</td>
+ <td>Pituitary</td>
+ <td>85</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>34</td>
+ <td>R7132P</td>
+ <td>BXD40</td>
+ <td>Pituitary</td>
+ <td>85</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>35</td>
+ <td>R7056P</td>
+ <td>BXD42</td>
+ <td>Pituitary</td>
+ <td>87</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>36</td>
+ <td>R7044P</td>
+ <td>BXD42</td>
+ <td>Pituitary</td>
+ <td>87</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>37</td>
+ <td>R7043P</td>
+ <td>BXD43</td>
+ <td>Pituitary</td>
+ <td>81</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>38</td>
+ <td>R7047P</td>
+ <td>BXD43</td>
+ <td>Pituitary</td>
+ <td>81</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>39</td>
+ <td>R7091P</td>
+ <td>BXD44</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>40</td>
+ <td>R7050P</td>
+ <td>BXD44</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>41</td>
+ <td>R7077P</td>
+ <td>BXD45</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>42</td>
+ <td>R7078P</td>
+ <td>BXD45</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>43</td>
+ <td>R7042P</td>
+ <td>BXD45</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>44</td>
+ <td>R7092P</td>
+ <td>BXD48</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>45</td>
+ <td>R7093P</td>
+ <td>BXD48</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>46</td>
+ <td>R7045P</td>
+ <td>BXD49</td>
+ <td>Pituitary</td>
+ <td>84</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>47</td>
+ <td>R7094P</td>
+ <td>BXD49</td>
+ <td>Pituitary</td>
+ <td>84</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>48</td>
+ <td>R7095P</td>
+ <td>BXD50</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>49</td>
+ <td>R7096P</td>
+ <td>BXD50</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>50</td>
+ <td>R7142P</td>
+ <td>BXD56</td>
+ <td>Pituitary</td>
+ <td>84</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>51</td>
+ <td>R7097P</td>
+ <td>BXD56</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>52</td>
+ <td>R7080P</td>
+ <td>BXD60</td>
+ <td>Pituitary</td>
+ <td>70</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>53</td>
+ <td>R7141P_RW204</td>
+ <td>BXD60</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>54</td>
+ <td>R7075P</td>
+ <td>BXD62</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>55</td>
+ <td>R7083P</td>
+ <td>BXD62</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>56</td>
+ <td>R7084P</td>
+ <td>BXD62</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>57</td>
+ <td>R7098P</td>
+ <td>BXD63</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>58</td>
+ <td>R7100P</td>
+ <td>BXD65</td>
+ <td>Pituitary</td>
+ <td>84</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>59</td>
+ <td>R7120P</td>
+ <td>BXD66</td>
+ <td>Pituitary</td>
+ <td>257</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>60</td>
+ <td>R7140P</td>
+ <td>BXD68</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>61</td>
+ <td>R7101P</td>
+ <td>BXD68</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>62</td>
+ <td>R7074P</td>
+ <td>BXD69</td>
+ <td>Pituitary</td>
+ <td>69</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>63</td>
+ <td>R7139P</td>
+ <td>BXD69</td>
+ <td>Pituitary</td>
+ <td>81</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>64</td>
+ <td>R7141P</td>
+ <td>BXD65</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>65</td>
+ <td>R7137P_RW112</td>
+ <td>BXD70</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>66</td>
+ <td>R7124P</td>
+ <td>BXD71</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>67</td>
+ <td>R7123P</td>
+ <td>BXD71</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>68</td>
+ <td>R7068P</td>
+ <td>BXD73</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>69</td>
+ <td>R7118P</td>
+ <td>BXD74</td>
+ <td>Pituitary</td>
+ <td>69</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>70</td>
+ <td>R7117P</td>
+ <td>BXD74</td>
+ <td>Pituitary</td>
+ <td>69</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>71</td>
+ <td>R7082P</td>
+ <td>BXD75</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>72</td>
+ <td>R7048P</td>
+ <td>BXD75</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>73</td>
+ <td>R7122P</td>
+ <td>BXD77</td>
+ <td>Pituitary</td>
+ <td>223</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>74</td>
+ <td>R7103P</td>
+ <td>BXD79</td>
+ <td>Pituitary</td>
+ <td>86</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>75</td>
+ <td>R7104P</td>
+ <td>BXD79</td>
+ <td>Pituitary</td>
+ <td>86</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>76</td>
+ <td>R7073P</td>
+ <td>BXD80</td>
+ <td>Pituitary</td>
+ <td>73</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>77</td>
+ <td>R7070P</td>
+ <td>BXD80</td>
+ <td>Pituitary</td>
+ <td>73</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>78</td>
+ <td>R7139P_RW138</td>
+ <td>BXD83</td>
+ <td>Pituitary</td>
+ <td>81</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>79</td>
+ <td>R7137P</td>
+ <td>BXD83</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>80</td>
+ <td>R7085P</td>
+ <td>BXD84</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>81</td>
+ <td>R7081P</td>
+ <td>BXD84</td>
+ <td>Pituitary</td>
+ <td>76</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>82</td>
+ <td>R7105P</td>
+ <td>BXD85</td>
+ <td>Pituitary</td>
+ <td>73</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>83</td>
+ <td>R7144P</td>
+ <td>BXD87</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>84</td>
+ <td>R7136P_RW196</td>
+ <td>BXD87</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>85</td>
+ <td>R7106P</td>
+ <td>BXD89</td>
+ <td>Pituitary</td>
+ <td>82</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>86</td>
+ <td>R7107P</td>
+ <td>BXD89</td>
+ <td>Pituitary</td>
+ <td>82</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>87</td>
+ <td>R7108P</td>
+ <td>BXD90</td>
+ <td>Pituitary</td>
+ <td>82</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>88</td>
+ <td>R7109P</td>
+ <td>BXD90</td>
+ <td>Pituitary</td>
+ <td>82</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>89</td>
+ <td>R7138P_RW170</td>
+ <td>BXD95</td>
+ <td>Pituitary</td>
+ <td>73</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>90</td>
+ <td>R7111P</td>
+ <td>BXD97</td>
+ <td>Pituitary</td>
+ <td>71</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>91</td>
+ <td>R7112P</td>
+ <td>BXD97</td>
+ <td>Pituitary</td>
+ <td>71</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>92</td>
+ <td>R7113P</td>
+ <td>BXD99</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>93</td>
+ <td>R7114P</td>
+ <td>BXD99</td>
+ <td>Pituitary</td>
+ <td>77</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>94</td>
+ <td>R7072P</td>
+ <td>BXD100</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>95</td>
+ <td>R7087P</td>
+ <td>BXD100</td>
+ <td>Pituitary</td>
+ <td>88</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>96</td>
+ <td>R7086P</td>
+ <td>BXD100</td>
+ <td>Pituitary</td>
+ <td>83</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>97</td>
+ <td>R7088P</td>
+ <td>BXD101</td>
+ <td>Pituitary</td>
+ <td>88</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>98</td>
+ <td>R7053P</td>
+ <td>BXD102</td>
+ <td>Pituitary</td>
+ <td>88</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>99</td>
+ <td>R7046P</td>
+ <td>BXD102</td>
+ <td>Pituitary</td>
+ <td>88</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td>100</td>
+ <td>R7090P</td>
+ <td>BXD103</td>
+ <td>Pituitary</td>
+ <td>78</td>
+ <td>F</td>
+ </tr>
+ <tr>
+ <td>101</td>
+ <td>R7067P</td>
+ <td>BXD103</td>
+ <td>Pituitary</td>
+ <td>78</td>
+ <td>M</td>
+ </tr>
+ </tbody>
+ </table>
+ </td>
+ </tr>
+ </tbody>
+</table>
diff --git a/general/datasets/Inia_pg_rma_ex_0612/citation.rtf b/general/datasets/Inia_pg_rma_ex_0612/citation.rtf new file mode 100644 index 0000000..1ef65cb --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/citation.rtf @@ -0,0 +1 @@ +<p>Contact RW Williams</p>
diff --git a/general/datasets/Inia_pg_rma_ex_0612/contributors.rtf b/general/datasets/Inia_pg_rma_ex_0612/contributors.rtf new file mode 100644 index 0000000..5178980 --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/contributors.rtf @@ -0,0 +1 @@ +<p>Mozhui K, Lu L, Adler A, Ingels J, Williams RW</p>
diff --git a/general/datasets/Inia_pg_rma_ex_0612/experiment-design.rtf b/general/datasets/Inia_pg_rma_ex_0612/experiment-design.rtf new file mode 100644 index 0000000..13175b5 --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/experiment-design.rtf @@ -0,0 +1,10 @@ +<p>Normative expression in the whole pituitary 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>QUALITY CONTROL DATA</p>
+
+<ol>
+ <li>737 probe sets with LRS of 46 or higher (LOD>10)</li>
+ <li>Highest LRS = 165.7</li>
+ <li>Review of top Mendelian transcripts consist with correct strain assignment</li>
+ <li>Final sex assignment is correct</li>
+</ol>
diff --git a/general/datasets/Inia_pg_rma_ex_0612/platform.rtf b/general/datasets/Inia_pg_rma_ex_0612/platform.rtf new file mode 100644 index 0000000..7057d48 --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/platform.rtf @@ -0,0 +1 @@ +<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_pg_rma_ex_0612/processing.rtf b/general/datasets/Inia_pg_rma_ex_0612/processing.rtf new file mode 100644 index 0000000..55aad2e --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/processing.rtf @@ -0,0 +1 @@ +<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_pg_rma_ex_0612/summary.rtf b/general/datasets/Inia_pg_rma_ex_0612/summary.rtf new file mode 100644 index 0000000..14a715d --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/summary.rtf @@ -0,0 +1,3 @@ +<p>Gene expression data for the whole pituitary across 52 strains of mice. Sex Balance: Sex of samples has been double-checked. As of July 2012, for 42 strains we have separate data for both males and females (usually one array each). Three strains (BXD45, 63, and 95) are only represented by female samples and two strains (BXD65 and BXD77) are only represented by male samples. Five other strains (BXD24, 66, 73, 85, 101) are may represent combined male and female samples. These unpublished data are apparently error-free based on a review and analysis of transcripts with Mendelian segregation patterns (as of July 20, 2012). The data set contains 751 eQTLs with LOD scores above 10 (LRS>46). Peak LRS of 165.9 for Record ID 10513604. Data for BXD70 are somewhat problematic (see 10444135 and 10467784), perhaps due to a bad array, strain assignment error, or residual heterozygozity. S Roy double-checked (July 22) and thinks that Sample R7141P is more likely to be BXD65.</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_pg_rma_ex_0612/tissue.rtf b/general/datasets/Inia_pg_rma_ex_0612/tissue.rtf new file mode 100644 index 0000000..3977f1e --- /dev/null +++ b/general/datasets/Inia_pg_rma_ex_0612/tissue.rtf @@ -0,0 +1 @@ +<p>Whole pituitary gland dissected by hand. Dissections by Khyobeni Mozhui, Jesse Ingels, and Adrienne Adler at UTHSC.</p>
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