Update dataset RTF Files.

9 files changed, 93 insertions, 0 deletions

diff --git a/general/datasets/El_bxdcdscwat_0216/acknowledgment.rtf b/general/datasets/El_bxdcdscwat_0216/acknowledgment.rtf
new file mode 100644
index 0000000..3fc4fc5
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/acknowledgment.rtf
@@ -0,0 +1,11 @@
+<blockquote>

+<table border="0" cellpadding="5" cellspacing="0" style="width:100%">

+	<tbody>

+		<tr>

+			<td>

+			<p>The authors&nbsp;thank Cristina Cartoni, S&eacute;bastien Lamy, and Charles Thomas at the Center of Phenogenomics (CPG, EPFL) for help in establishing and phenotyping the BXD mice. We thank the Molecular Resource Center of Excellence at The University of Tennessee Health Science Center processing all microarrays.</p>

+			</td>

+		</tr>

+	</tbody>

+</table>

+</blockquote>

diff --git a/general/datasets/El_bxdcdscwat_0216/cases.rtf b/general/datasets/El_bxdcdscwat_0216/cases.rtf
new file mode 100644
index 0000000..f54f4f2
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/cases.rtf
@@ -0,0 +1,11 @@
+<blockquote>

+<table border="0" cellpadding="5" cellspacing="0" style="width:100%">

+	<tbody>

+		<tr>

+			<td>

+			<p>40 strains of the BXD family (BXD43 &ndash; BXD103) and both parental strains (C57BL/6 and DBA/2) were born and raised at the EPFL in Switzerland prior to inclusion in this study. For each strain, 10 male animals were born and then separated evenly into two cohorts at 8 weeks of age: 5 animals per strain on a chow diet (6% kcal/fat, 20% protein, 74% carbohydrate) and 5 animals per strain on high fat diet (60% kcal/fat, 20% protein, 20% carbohydrate). Animals adjusted to the diet for 8 weeks, and then an intensive phenotyping metabolic phenotyping protocol was followed from 16 to 24 weeks of age (respiration, cold tolerance, oral glucose response, VO2max exercise, voluntary exercise, basal activity). Animals were communally housed until the last 5 weeks of the experiment, allowing the animals to rest and reduce the direct expression effects of the phenotyping tests. Animals were fasted overnight prior to sacrifice, which occurred between&nbsp;9am and 11am&nbsp;after isoflurane anesthesia and perfusion. Subcuteaneous white adipose tissue was collected near the end of the sacrifice pipeline, occurring an estimated 10&plusmn;2 minutes after sacrifice. The tissue was weighed and then placed in a storage tube in liquid nitrogen.</p>

+			</td>

+		</tr>

+	</tbody>

+</table>

+</blockquote>

diff --git a/general/datasets/El_bxdcdscwat_0216/citation.rtf b/general/datasets/El_bxdcdscwat_0216/citation.rtf
new file mode 100644
index 0000000..249a454
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/citation.rtf
@@ -0,0 +1,11 @@
+<blockquote>

+<table border="0" cellpadding="5" cellspacing="0" style="width:100%">

+	<tbody>

+		<tr>

+			<td>

+			<p>Unpublished data. Please contact the laboratory of Johan Auwerx at the EPFL (<a href="http://auwerx-lab.epfl.ch/" target="_blank">http://auwerx-lab.epfl.ch/</a>)&nbsp;for early access.&nbsp;</p>

+			</td>

+		</tr>

+	</tbody>

+</table>

+</blockquote>

diff --git a/general/datasets/El_bxdcdscwat_0216/contributors.rtf b/general/datasets/El_bxdcdscwat_0216/contributors.rtf
new file mode 100644
index 0000000..ae951c8
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/contributors.rtf
@@ -0,0 +1,11 @@
+<blockquote>

+<table border="0" cellpadding="5" cellspacing="0" style="width:100%">

+	<tbody>

+		<tr>

+			<td>

+			<p>Williams EG, Jha P, Hao L, Andreux PA, Auwerx J</p>

+			</td>

+		</tr>

+	</tbody>

+</table>

+</blockquote>

diff --git a/general/datasets/El_bxdcdscwat_0216/experiment-design.rtf b/general/datasets/El_bxdcdscwat_0216/experiment-design.rtf
new file mode 100644
index 0000000..b417b79
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/experiment-design.rtf
@@ -0,0 +1,11 @@
+<blockquote>

+<table border="0" cellpadding="5" cellspacing="0" style="width:100%">

+	<tbody>

+		<tr>

+			<td>

+			<p>All animals were communally housed by strain until phenotyping and fed a chow diet (CD; (Harlan 2018; 6% kCal/fat, 20% kCal/protein, 74% kCal/carbohydrate) throughout life after weaning until sacrifice at around 29 weeks of age, or a high fat diet (HFD; Harlan TD.06414 60% kcal/fat, 20% protein, 20% carbohydrate) after 8 weeks of age until sacrifice around 29 weeks of age. All BXD strains (BXD43&ndash;103) were originally sourced from the vivarium at the University of Tennessee Health Science Center (Memphis, TN, USA) then bred for two or more generations until progeny entered the phenotyping colony. C57BL/6J and DBA/2J were sourced from Janvier, which re-sources its &ldquo;J&rdquo; lines every 10 generations from The Jackson Laboratory. For tissue collection on CD and HFD BXD cohorts, animals were sacrificed under isoflurane anesthesia and cardiac perfusion after an overnight fast. High fat diet treatment and two day isolation for the recording experiment were considered as having low impact on the animals&rsquo; welfare, while all other measurements and conditions were considered as having no negative impact. All research was approved by the Swiss cantonal veterinary authorities of Vaud under licenses 2257.0 and 2257.1.&nbsp;</p>

+			</td>

+		</tr>

+	</tbody>

+</table>

+</blockquote>

diff --git a/general/datasets/El_bxdcdscwat_0216/platform.rtf b/general/datasets/El_bxdcdscwat_0216/platform.rtf
new file mode 100644
index 0000000..066be8d
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/platform.rtf
@@ -0,0 +1,5 @@
+<p><a href="http://www.affymetrix.com/catalog/prod870009/AFFY/Mouse+Transcriptome+Assay+1.0#1_1">GeneChip Mouse Transcriptome Assay 1.0</a></p>

+

+<p>All arrays were Affymetrix Mouse Transcriptome Assay 1.0, prepared and run simultaneously in a single batch in January 2016 by Lorne Rose at the University of Tennessee Health Science Center.</p>

+

+<p>Data error checked by RW Williams and&nbsp;David Ashbrook (March 2019). Numerous strain assignment corrections to HFD limb of study. Finally eQTL analysis validates both CD and HFD components.&nbsp;</p>

diff --git a/general/datasets/El_bxdcdscwat_0216/processing.rtf b/general/datasets/El_bxdcdscwat_0216/processing.rtf
new file mode 100644
index 0000000..5dbb444
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/processing.rtf
@@ -0,0 +1,11 @@
+<blockquote>

+<table border="0" cellpadding="5" cellspacing="0" style="width:100%">

+	<tbody>

+		<tr>

+			<td>

+			<p>In general, the array data that we put in GeneNetwork has be logged and then z normalized, but instead of leaving the mean at 0 and the standard deviation of 1 unit, we shift up to a mean of 8 units and increase the spread by having an standard deviation of 2 units (what we call 2Z + 8 normalized data). This removes negative values from the tables.</p>

+			</td>

+		</tr>

+	</tbody>

+</table>

+</blockquote>

diff --git a/general/datasets/El_bxdcdscwat_0216/summary.rtf b/general/datasets/El_bxdcdscwat_0216/summary.rtf
new file mode 100644
index 0000000..6c2d77a
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/summary.rtf
@@ -0,0 +1,11 @@
+<blockquote>

+<table border="0" cellpadding="5" cellspacing="0" style="width:100%">

+	<tbody>

+		<tr>

+			<td>

+			<p>The BXD genetic reference population is a recombinant inbred panel descended from crosses between the C57BL/6 (B6) and DBA/2 (D2) strains of mice, which segregate for about 5 million sequence variants. Recently, some these variants have been established with effects on general metabolic phenotypes such as glucose response and bone strength. In this study, we examined both genetic variants across 40 strains of BXD and the two founder lines, in addition&nbsp;to a major environmental influence&mdash;long term feeding with chow diet (CD) or high fat diet (HFD)&mdash;to see how metabolic gene expression varies by genotype and environment, and gene-by-environment interactions. The basic heart phenotypes quantified in these cohorts were not affected by HFD feeding (e.g. blood pressure and heart rate).&nbsp;</p>

+			Microarray data for four other tissues in the exact same cohorts was processed and is in GeneNetwork: Heart, Liver, Muscle [Quadriceps], and Adipose [Brown]. Proteomic data for one other tissue in the exact same cohorts was processed and is in GeneNetwork: Liver. Metabolomic data for two tissues in the same cohorts was processed and is in GeneNetwork: Liver and Muscle [Quadriceps]. Brown Adipose was only run in CD cohorts, while all other datasets were run on both diets. All phenotype data associated with these animals can be found by searching Phenotypes for the code &ldquo;LISP3&rdquo;. Note that some traits are still private, while others have been published.</td>

+		</tr>

+	</tbody>

+</table>

+</blockquote>

diff --git a/general/datasets/El_bxdcdscwat_0216/tissue.rtf b/general/datasets/El_bxdcdscwat_0216/tissue.rtf
new file mode 100644
index 0000000..e595c55
--- /dev/null
+++ b/general/datasets/El_bxdcdscwat_0216/tissue.rtf
@@ -0,0 +1,11 @@
+<blockquote>

+<table border="0" cellpadding="5" cellspacing="0" style="width:100%">

+	<tbody>

+		<tr>

+			<td>

+			<p>Subcuteaneous WAT was later shattered in liquid nitrogen, and around 100 mg was taken for preparation. All ~5 animals per cohort had their RNA prepared, and then were pooled evenly (by &micro;g of RNA) into a single RNA sample for each cohort. The pooled RNA samples were then purified using RNEasy, then sent out for array analysis. All RIN values were &gt; 8.0. RNA was prepared in the summer of 2013, while the RNEasy cleanup occurred in the winter of 2015; unlike the other tissues run as a part of this study, these RNA samples spent a significant time in the -80&deg; freezers. However, the samples only underwent one freeze&mdash;thaw cycle.</p>

+			</td>

+		</tr>

+	</tbody>

+</table>

+</blockquote>