diff options
Diffstat (limited to 'general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112')
3 files changed, 272 insertions, 0 deletions
diff --git a/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/cases.rtf b/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/cases.rtf new file mode 100644 index 0000000..2f0fdc0 --- /dev/null +++ b/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/cases.rtf @@ -0,0 +1,245 @@ +<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>Original Strain</td> + <td>Corrected Strain</td> + <td>Sex</td> + <td>Age</td> + </tr> + <tr> + <td>1</td> + <td>BXD13_batch2</td> + <td>BXD18</td> + <td>M</td> + <td>67</td> + </tr> + <tr> + <td>2</td> + <td>BXD15_batch2</td> + <td>BXD15</td> + <td>F</td> + <td>62</td> + </tr> + <tr> + <td>3</td> + <td>BXD18_batch2</td> + <td>BXD19</td> + <td>F</td> + <td>65</td> + </tr> + <tr> + <td>4</td> + <td>BXD24_batch2</td> + <td>BXD24</td> + <td>F</td> + <td>63</td> + </tr> + <tr> + <td>5</td> + <td>BXD36_batch2</td> + <td>BXD45 removed</td> + <td>M</td> + <td>67</td> + </tr> + <tr> + <td>6</td> + <td>BXD39_batch2</td> + <td>BXD39</td> + <td>F</td> + <td>60</td> + </tr> + <tr> + <td>7</td> + <td>BXD42_batch2</td> + <td>BXD43</td> + <td>F</td> + <td>67</td> + </tr> + <tr> + <td>8</td> + <td>BXD43_batch2</td> + <td>BXD42</td> + <td>F</td> + <td>60</td> + </tr> + <tr> + <td>9</td> + <td>BXD45_batch2</td> + <td>BXD45</td> + <td>F</td> + <td>60</td> + </tr> + <tr> + <td>10</td> + <td>BXD50_batch2</td> + <td>BXD50</td> + <td>F</td> + <td>57</td> + </tr> + <tr> + <td>11</td> + <td>BXD51_batch2</td> + <td>BXD55</td> + <td>F</td> + <td>59</td> + </tr> + <tr> + <td>12</td> + <td>BXD55_batch2</td> + <td>BXD51</td> + <td>F</td> + <td>61</td> + </tr> + <tr> + <td>13</td> + <td>BXD56_batch2</td> + <td>BXD56</td> + <td>F</td> + <td>67</td> + </tr> + <tr> + <td>14</td> + <td>BXD6_batch2</td> + <td>BXD6</td> + <td>F</td> + <td>59</td> + </tr> + <tr> + <td>15</td> + <td>BXD8_batch2</td> + <td>BXD9</td> + <td>F</td> + <td>62</td> + </tr> + <tr> + <td>16</td> + <td>BXD9_batch2</td> + <td>BXD8</td> + <td>M</td> + <td>70</td> + </tr> + <tr> + <td>17</td> + <td>BXD14_batch3</td> + <td>BXD40</td> + <td>F</td> + <td>76</td> + </tr> + <tr> + <td>18</td> + <td>BXD16_batch3</td> + <td>BXD19</td> + <td>M</td> + <td>74</td> + </tr> + <tr> + <td>19</td> + <td>BXD32_batch3</td> + <td>BXD32</td> + <td>M</td> + <td>54</td> + </tr> + <tr> + <td>20</td> + <td>BXD38_batch3</td> + <td>BXD38</td> + <td>F</td> + <td>102</td> + </tr> + <tr> + <td>21</td> + <td>BXD40_batch3</td> + <td>BXD14</td> + <td>M</td> + <td>81</td> + </tr> + <tr> + <td>22</td> + <td>BXD48_batch3</td> + <td>BXD48</td> + <td>M</td> + <td>68</td> + </tr> + <tr> + <td>23</td> + <td>BXD60_batch3</td> + <td>BXD60</td> + <td>F</td> + <td>64</td> + </tr> + <tr> + <td>24</td> + <td>BXD66_batch3</td> + <td>BXD66</td> + <td>M</td> + <td>61</td> + </tr> + <tr> + <td>25</td> + <td>BXD69_batch3</td> + <td>BXD69</td> + <td>F</td> + <td>66</td> + </tr> + <tr> + <td>26</td> + <td>BXD70_batch3</td> + <td>BXD70</td> + <td>M</td> + <td>72</td> + </tr> + <tr> + <td>27</td> + <td>BXD29m_batch4</td> + <td>BXD1</td> + <td>F</td> + <td>60</td> + </tr> + <tr> + <td>28</td> + <td>BXD29n_batch4</td> + <td>BXD29</td> + <td>F</td> + <td>344</td> + </tr> + <tr> + <td>29</td> + <td>BXD34_batch4</td> + <td>BXD34</td> + <td>F</td> + <td>108</td> + </tr> + <tr> + <td>30</td> + <td>BXD49_batch4</td> + <td>BXD49</td> + <td>M</td> + <td>76</td> + </tr> + <tr> + <td>31</td> + <td>BXD65_batch4</td> + <td>BXD29</td> + <td>F</td> + <td>58</td> + </tr> + <tr> + <td>32</td> + <td>BXD22_batch6</td> + <td>BXD22</td> + <td>F</td> + <td>67</td> + </tr> + </tbody> + </table> + </td> + </tr> + </tbody> +</table> +</blockquote> diff --git a/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/notes.rtf b/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/notes.rtf new file mode 100644 index 0000000..c16bd50 --- /dev/null +++ b/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/notes.rtf @@ -0,0 +1,23 @@ +<p>RNA sequencing for BXD strains on SOLiD by David Li.<br /> +All Bam files alignment done by Xusheng Wang<br /> +Aligned files were uploaded to Partek Genomic Suite 6.5 (version 6.10.0810) and processed by K Mozhui<br /> +Normalization: RPKM (reads per kilobase per million mapped reads)<br /> +Batch effect due to low exonic reads for batch 2</p> + +<p>Revision 1.6 Untrimmed (current) LRS=(23 999) -><strong>350</strong> records<br /> +Max LRS = <strong>102.6</strong> Record Id:uthsc_nr_015498, Gene Symbol:1500004A13Rik **Note: 1 sample BXD45 and BXD34 removed. BXD41 switched to BXD1 as a second posible candidate.</p> + +<p>Revision 1.5 Untrimmed LRS=(23 999) -><strong>268</strong> records<br /> +Max LRS = <strong>80.0</strong> Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1 **Note: 1 sample BXD45 removed. BXD41 switched to BXD1 as a second posible candidate.</p> + +<p>Revision 1.4 Untrimmed LRS=(23 999) -><strong>246</strong> records<br /> +Max LRS = <strong>80.0</strong> Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1 **Note: 1 sample BXD45 removed and keep BXD41</p> + +<p>Revision 1.3 Untrimmed LRS=(23 999) -><strong>233</strong> records<br /> +Max LRS = <strong>80.7</strong> Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1</p> + +<p>Revision 1.2 Untrimmed LRS=(23 999) -><strong>190</strong> records<br /> +Max LRS = <strong>56.9</strong> Record Id:uthsc_nr_003513, Gene Symbol:Neat1</p> + +<p>Revision 1 Untrimmed LRS=(23 999) -><strong>126</strong> records<br /> +Max LRS = <strong>35.3</strong> Record Id:uthsc_nm_001113412, Gene Symbol:Fggy</p> diff --git a/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/summary.rtf b/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/summary.rtf new file mode 100644 index 0000000..82080d4 --- /dev/null +++ b/general/datasets/UTHSC_BXD_WB_RNASeqtrim1_1112/summary.rtf @@ -0,0 +1,4 @@ +<ul> + <li>UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM <strong>Untrimmed</strong></li> + <li>UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM <strong>Trimmed</strong> dataset have been re-normalized by forcing values down to zero at level of individual mRNA seq assay.</li> +</ul> |