Update dataset RTF Files.

7 files changed, 0 insertions, 45 deletions

diff --git a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/acknowledgment.rtf b/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/acknowledgment.rtf
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--- a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/acknowledgment.rtf
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-<p>This work done in collaboration with RTI under a special pilot project grant from the RCMRC Center.</p>

-

-<p>1. Dr. Susan Sumner. PI of grant</p>

-

-<p>2. Dr. Robert Clarke. Lead investigator on this project</p>

-

-<p>3. Surja Dhungana</p>

diff --git a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/cases.rtf b/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/cases.rtf
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--- a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/cases.rtf
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-<p>All animals are females sacrificed&nbsp;as part of an NIA grant to RW Williams to study effects of diet on aging (longevity) &nbsp;in the BXD strains. A subset of females were sacrificed at specific ages for tissue harvesting and fecal pelltets from these animals were removed from the large intestine by K. Mozhui&nbsp;and snap frozen in liquid nitrogen prior to shipping to RTI.</p>

-

-<p>Three large data sets in GeneNetwork with a common set of 4091 metabolite entries per data set (high fat, chow diet, and combined) and for as many as 18 strains.</p>

diff --git a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/experiment-design.rtf b/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/experiment-design.rtf
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--- a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/experiment-design.rtf
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-<p><strong>Sample Preparation Summary</strong></p>

-

-<ul>

-	<li>Feces were extracted in 95:5 water:methanol</li>

-	<li>Extracts were prepared for UPLC-QTOF-MS analysis</li>

-</ul>

-

-<p><strong>Instruments for LC-MS Analysis</strong><br />

-Waters SYNAPT G2 QTOF with Acquity UPLC (Waters Corporation, MA)<br />

-MS data collected over 50-1000 m/z was collected in the positive and negative ion modes.</p>

-

-<p><strong>UPLC-MS Solutions(Reversed Phase)</strong><br />

-Mobile Phase A (Reversed-Phase)&mdash;Water with 0.1% Formic Acid<br />

-Mobile Phase B (Reversed-Phase)&mdash;Methanol with 0.1% Formic Acid<br />

-Column: Waters Acquity BEH HSS T3, 2.1 x 100 mm at 50 &deg;C</p>

-

-<p>&nbsp;</p>

diff --git a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/notes.rtf b/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/notes.rtf
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--- a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/notes.rtf
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-<p>For symbols of metabolites if the differences were greater than .0003 proportional m/z units (m/z difference divided by m/z value) then the symbol was labeled &quot;circa&quot; after the atomic composition.&nbsp;</p>

-

-<p>For description of metabolites if the proportional difference of the m/z ratio between Evan&#39;s EPFL Polar metabolite&nbsp;assignments and RTI assignments was very low (&lt;.0001 proportional m/z units) then the symbol and description was taken directly from Evan&#39;s metabolite file, but if differences were between 0.0001 and about .0003 proportional m/z units then the descriptions were labeled &quot;Putative&quot; . If the differences were greater than .0003 units, then the descriptions were labeled &quot;Provisional&quot;. For example,<span style="background-color:rgb(238, 238, 238); color:rgb(34, 34, 34); font-family:verdana,geneva,lucida,lucida grande,arial,helvetica">&nbsp;&quot;P</span><span style="color:rgb(34, 34, 34); font-family:verdana,geneva,lucida,lucida grande,arial,helvetica; font-size:12px">rovisional assignment. Vanilpyruvic acid is a catecholamine metabolite and precursor to vanilactic acid. Accumulation in urine is indicative of Aromatic L-aminoacid decarboxylase deficiency (PMID 16288991).&quot;&nbsp;</span></p>

-

-<p>&nbsp;by Rob Williams and Arthur Centeno, Aug 25, 2014</p>

diff --git a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/platform.rtf b/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/platform.rtf
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--- a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/platform.rtf
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-<p>This is LC-MS data. Analysis exploited a&nbsp;Chenomx library at RTI with many updated metabolite identifications from the standard Chenomx library. Note that a&nbsp;single m/z ratio can correspond to&nbsp;multiple metabolites.</p>

diff --git a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/summary.rtf b/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/summary.rtf
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--- a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/summary.rtf
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@@ -1,11 +0,0 @@
-<p>The goal of this project is to study expression of a large set of defined and undefined metabolites in fecal samples from a genetically diverse set of BXD mouse strains (females) raised either on a high fat diet or low fat diet. Samples were taken from animals at sacrifices directly from the large intestine.</p>

-

-<p>Aim: Effect of genetics and diet on fecal metabolomics</p>

-

-<p>Use UPLC-MS Broad Spectrum Metabolomics to study:</p>

-

-<ul>

-	<li>Mice fecal samples</li>

-</ul>

-

-<p>To capture the most signal, all samples were analyzed under positive and negative ion mode using a reversed-phase separation.</p>

diff --git a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/tissue.rtf b/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/tissue.rtf
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--- a/general/datasets/RTI_RCMRC_BXDFecMetHFlog0814/tissue.rtf
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-<p>Fresh fecal pellets taken directly at dissection from the lower GI tract by Dr. Khyobeni Mozhui.</p>