From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001
From: Bonface
Date: Fri, 9 Feb 2024 09:41:28 -0600
Subject: Update dataset RTF Files.

---
 general/datasets/UTHSC_BXD_WB_RNASeq1112/cases.rtf | 245 +++++++++++++++++++++
 general/datasets/UTHSC_BXD_WB_RNASeq1112/notes.rtf |  23 ++
 .../datasets/UTHSC_BXD_WB_RNASeq1112/specifics.rtf |   1 +
 .../datasets/UTHSC_BXD_WB_RNASeq1112/summary.rtf   |   4 +
 4 files changed, 273 insertions(+)
 create mode 100644 general/datasets/UTHSC_BXD_WB_RNASeq1112/cases.rtf
 create mode 100644 general/datasets/UTHSC_BXD_WB_RNASeq1112/notes.rtf
 create mode 100644 general/datasets/UTHSC_BXD_WB_RNASeq1112/specifics.rtf
 create mode 100644 general/datasets/UTHSC_BXD_WB_RNASeq1112/summary.rtf

(limited to 'general/datasets/UTHSC_BXD_WB_RNASeq1112')

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) -&gt;<strong>350</strong>&nbsp;records<br />
+Max LRS =&nbsp;<strong>102.6</strong>&nbsp;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&nbsp;LRS=(23 999) -&gt;<strong>268</strong>&nbsp;records<br />
+Max LRS =&nbsp;<strong>80.0</strong>&nbsp;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&nbsp;LRS=(23 999) -&gt;<strong>246</strong>&nbsp;records<br />
+Max LRS =&nbsp;<strong>80.0</strong>&nbsp;Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1 **Note: 1 sample BXD45 removed and keep BXD41</p>
+
+<p>Revision 1.3 Untrimmed&nbsp;LRS=(23 999) -&gt;<strong>233</strong>&nbsp;records<br />
+Max LRS =&nbsp;<strong>80.7</strong>&nbsp;Record Id:uthsc_nm_001039533, Gene Symbol:Pdxdc1</p>
+
+<p>Revision 1.2 Untrimmed&nbsp;LRS=(23 999) -&gt;<strong>190</strong>&nbsp;records<br />
+Max LRS =&nbsp;<strong>56.9</strong>&nbsp;Record Id:uthsc_nr_003513, Gene Symbol:Neat1</p>
+
+<p>Revision 1 Untrimmed&nbsp;LRS=(23 999) -&gt;<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 &gt; 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>&nbsp;dataset have been re-normalized by forcing values down to zero at level of individual mRNA seq assay.</li>
+</ul>
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