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authorBonface2024-02-13 23:52:26 -0600
committerMunyoki Kilyungi2024-08-09 13:30:43 +0300
commitb2feda451ccfbeaed02dce9088d6dd228cf15861 (patch)
tree3dd2883524985114070a7770cd2e9f9bd7eb1848 /general/datasets/Epfl_lisp_livpmetlog2cd1213
parentd029d5d7f8ead1f1de8d318045004a4a6f68f5fb (diff)
downloadgn-docs-b2feda451ccfbeaed02dce9088d6dd228cf15861.tar.gz
Update dataset RTF Files.
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diff --git a/general/datasets/Epfl_lisp_livpmetlog2cd1213/cases.rtf b/general/datasets/Epfl_lisp_livpmetlog2cd1213/cases.rtf
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+<p>For liver metabolites, livers were perfused, frozen in liquid nitrogen, and then shattered in liquid nitrogen with a mortar and pestle at a later date. Several pieces of shattered liver totalling ~100 milligrams were collected then homogenized in 1mL 70% Ethanol at -20&deg;C. Metabolites were extracted by adding 7mL 70% Ethanol at 75&deg;C for 2 min. Extracts were centrifuged for 10 minutes at 4,000 rpm at 4&deg;C. Clean metabolites extracts were dried in a vacuum centrifuge and re-suspended in double-distilled H2O with volume according to the weight of the extracted liver piece. Quantification of metabolites was performed on an Agilent 6550 QTOF instrument by flow injection analysis time-of-flight mass spectrometry (see: PMID 21830798). All samples were injected in duplicates. Ions were annotated based on their accurate mass and the Human Metabolome Database reference list (see: PMID 23161693) allowing a tolerance of 0.001 Da. Unknown ions and those annotated as adducts were discarded. Theoretical m/z ratios&mdash;beyond the significant digits from the measurement sensitivity&mdash;are used as the unique index in the online data on GeneNetwork. For example, deprotonated fumarate corresponds to 115.0036897_MZ, malate to 133.0142794_MZ, &alpha;-ketoglutarate to 145.0141831_MZ, and D2HG to 147.0298102_MZ.</p>
diff --git a/general/datasets/Epfl_lisp_livpmetlog2cd1213/processing.rtf b/general/datasets/Epfl_lisp_livpmetlog2cd1213/processing.rtf
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+<p>GeneNetwork displays only the strain averages &plusmn; SEM for each metabolite. To obtain the individual data for each animal, please use the link above under (<strong>Download datasets and supplementary data files)</strong>. Note that this contains two entries for each animal: these are technical replicates.&nbsp;</p>
+
+<p>The&nbsp;<em>very</em>&nbsp;raw spectral data from the mass spectrometer can be downloaded on MassIVE (&nbsp;<a href="http://massive.ucsd.edu/ProteoSAFe/static/massive.jsp?redirect=auth" target="_blank">http://massive.ucsd.edu/ProteoSAFe/static/massive.jsp?redirect=auth</a>&nbsp;)&nbsp;under the identifier MSV000079411. This spectral data is for all 290 individual animals, and it includes two technical replicates for each individual, for a total of 580 runs. The file size is 102 GB and we do not recommend downloading this unless you are specifically interested in re-analyzing the spectra from scratch and looking into the granular details of mass spectrometry metabolomics.</p>
diff --git a/general/datasets/Epfl_lisp_livpmetlog2cd1213/summary.rtf b/general/datasets/Epfl_lisp_livpmetlog2cd1213/summary.rtf
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+<p>We identified 979 unique metabolite features based on mass-charge ratios (m/z) using flow-injection ToF-MS, respectively. Of these features, 699 could be attributed to a single metabolite, including in cases where of the two &ldquo;possible&rdquo; enantiomers, one is clearly far more predominant than the other (e.g. L versus D amino acids). The remaining 280 metabolites were &ldquo;clusters&rdquo; with no clear predominant feature&mdash;for example, the &ldquo;glucose&rdquo; metabolite measurements could not be separated from fructose, galactose, or mannose measurements, as all share the same m/z. The &ldquo;main&rdquo; metabolite, as well as all possible alternatives are listed with the data on&nbsp;<a href="http://genenetwork.org/" target="_blank">GeneNetwork.org</a>&nbsp;for the raw file download (press the &ldquo;INFO&rdquo; button next to the dataset on the main search page and download the dataset and supplemental data files).</p>