diff options
| author | Bonface | 2024-02-15 06:09:54 -0600 |
|---|---|---|
| committer | Munyoki Kilyungi | 2024-08-09 13:30:43 +0300 |
| commit | e34e7da50fc0ff5ed41e8bdaf2b1d41c9e9cf534 (patch) | |
| tree | 67c6bdeb413af7d1dd6c4d02f37b206850a78531 /general/datasets/UTHSC_BXD_WB_RNASeq1112 | |
| parent | b2feda451ccfbeaed02dce9088d6dd228cf15861 (diff) | |
| download | gn-docs-e34e7da50fc0ff5ed41e8bdaf2b1d41c9e9cf534.tar.gz | |
Update dataset RTF Files.
Diffstat (limited to 'general/datasets/UTHSC_BXD_WB_RNASeq1112')
4 files changed, 0 insertions, 273 deletions
diff --git a/general/datasets/UTHSC_BXD_WB_RNASeq1112/cases.rtf b/general/datasets/UTHSC_BXD_WB_RNASeq1112/cases.rtf deleted file mode 100644 index 2f0fdc0..0000000 --- a/general/datasets/UTHSC_BXD_WB_RNASeq1112/cases.rtf +++ /dev/null @@ -1,245 +0,0 @@ -<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 deleted file mode 100644 index c16bd50..0000000 --- a/general/datasets/UTHSC_BXD_WB_RNASeq1112/notes.rtf +++ /dev/null @@ -1,23 +0,0 @@ -<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 deleted file mode 100644 index 8e3eb6f..0000000 --- a/general/datasets/UTHSC_BXD_WB_RNASeq1112/specifics.rtf +++ /dev/null @@ -1 +0,0 @@ -<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 deleted file mode 100644 index 82080d4..0000000 --- a/general/datasets/UTHSC_BXD_WB_RNASeq1112/summary.rtf +++ /dev/null @@ -1,4 +0,0 @@ -<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> |