Summary of Study ST001616
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001039. The data can be accessed directly via it's Project DOI: 10.21228/M8D400 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001616 |
| Study Title | Unique metabolomic profile of skeletal muscle in chronic limb threatening ischemia (aqueous phase samples ) |
| Study Type | NMR |
| Study Summary | This project is focused on a cross-sectional analysis of non-PAD controls and CLTI patients undergoing either a vascular intervention or undergoing limb amputation was performed and involved a detailed assessment of the limb muscle metabolome using HR-MAS and solution state NMR spectroscopy. It was hypothesized that patients undergoing limb amputation would present with altered muscle metaolite features compared with non-PAD controls. |
| Institute | University of Florida |
| Department | Applied Physiology and Kinesiology |
| Laboratory | Rm 42 and Rm 43 |
| Last Name | Ryan |
| First Name | Terence |
| Address | University of Florida, Applied Physiology and Kinesiology, 1864 stadium RD, Gainesville, FL 32611 |
| ryant@ufl.edu | |
| Phone | 352-294-1700 |
| Submit Date | 2020-11-30 |
| Num Groups | 3 |
| Total Subjects | 30 |
| Num Males | 25 |
| Num Females | 5 |
| Study Comments | PAD metabolomic study via NMR. A detailed assessment of the limb muscle metabolome using semi-solid and solution state NMR spectroscopy |
| Publications | Journal of Clinical Medicine |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2021-05-30 |
| Release Version | 1 |
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Sample Preparation:
| Sampleprep ID: | SP001699 |
| Sampleprep Summary: | Extraction. Both polar and non-polar metabolites were extracted from the gastrocnemius muscle specimens using FOLCH extraction. In brief, wet weigh of the frozen tissues were determined and immediately homogenized in 1 mL of ice-cold methanol using a PowerLyzer 24 Homogenizer (QIAGEN Group, Hilden, Germany). All enzymatic activities are halted once the sample was homogenized in the methanol. Homogenization was followed by centrifugation (13.2K r.p.m., 4 oC, 30 minutes) and supernatant was transferred into a new glass vial consisting a mixture of 3 mL of ice-cold chloroform and methanol (2:1 v/v) ratio. The cold mixture was vortexed for several minutes and left in an ice bath 15 minutes to allow for phase separation. Next, 1 mL of ice-cold 0.9% saline was added to the mixture followed by vigorous mixing. The mixture was again left in the ice bath for 45 minutes for phase separation. The upper methanol/water layer was transferred to a new falcon tube. To the lower chloroform layer, 1 mL of ice-cold 0.9% saline was added and all steps were followed as mentioned above. Following a 45-minute incubation, upper methanol/water layer was again transferred to the previous falcon tube and dried using a Labconco freeze drier (Labconco Corporation, MO, USA). The chloroform layer was dried under a stream of nitrogen gas. The dried samples (both aqueous and organic phases) were stored at -80 oC until resuspension for NMR experiments. Lyophilized aqueous phase samples were re-suspended in 50 µL of 50 mM phosphate buffer (pH 7.2) consisting 2 mM of EDTA along with 0.2% NaN3 and 0.5 mM D6-DSS in 100% deuterated environment. |
| Processing Method: | Lyophilization and Homogenization |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Modified FOLCH extraction for one set of samples |
| Extract Storage: | -80℃ |
| Sample Resuspension: | In 50 microliter of 50 mM phosphate buffer (pH 7.2) with 2 mM EDTA, 0.5 mM DSS and 0.2% sodium azide for aqueous phase samples. |
| Sample Spiking: | 0.5 mM of DSS for aqueous phase samples |
