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/Uthsc_bxd_wb_rnaseq1112 | |
| parent | d029d5d7f8ead1f1de8d318045004a4a6f68f5fb (diff) | |
| download | gn-docs-b2feda451ccfbeaed02dce9088d6dd228cf15861.tar.gz | |
Update dataset RTF Files.
Diffstat (limited to 'general/datasets/Uthsc_bxd_wb_rnaseq1112')
4 files changed, 273 insertions, 0 deletions
diff --git a/general/datasets/Uthsc_bxd_wb_rnaseq1112/cases.rtf b/general/datasets/Uthsc_bxd_wb_rnaseq1112/cases.rtf new file mode 100644 index 0000000..2f0fdc0 --- /dev/null +++ b/general/datasets/Uthsc_bxd_wb_rnaseq1112/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_rnaseq1112/notes.rtf b/general/datasets/Uthsc_bxd_wb_rnaseq1112/notes.rtf new file mode 100644 index 0000000..c16bd50 --- /dev/null +++ b/general/datasets/Uthsc_bxd_wb_rnaseq1112/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_rnaseq1112/specifics.rtf b/general/datasets/Uthsc_bxd_wb_rnaseq1112/specifics.rtf new file mode 100644 index 0000000..8e3eb6f --- /dev/null +++ b/general/datasets/Uthsc_bxd_wb_rnaseq1112/specifics.rtf @@ -0,0 +1 @@ +<p>Note: March 2019: now actually 449 transcripts/genes with LRS > 23 and peak LRS is still 102.6.</p>
diff --git a/general/datasets/Uthsc_bxd_wb_rnaseq1112/summary.rtf b/general/datasets/Uthsc_bxd_wb_rnaseq1112/summary.rtf new file mode 100644 index 0000000..82080d4 --- /dev/null +++ b/general/datasets/Uthsc_bxd_wb_rnaseq1112/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>
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