bariatric: Bariatric surgery data
In kimsche/MetaboMate: All you need for NMR-based metabolic profiling with R!
Description
Usage
Format
Details
Author(s)
Source
References
Description
Metabolic profiling NMR dataset of murine urine samples before and after undergoing bariatric surgery (Roux-en-Y gastric bypass).
Usage
1
Format
A list with three elements:
- X.pqn
Matrix of pre-processed Proton NMR spectra with rows representing spectra
- ppm
Chemical shift vector in ppm with its length equals the number of columns in X.pqn
- meta
Spectrometer metadata
Details
One dimensional proton NMR spectra of murine urine samples, acquired on a Bruker Avance III spectrometer (Bruker, Rheinstetten, Germany) operating at a frequency of 600.13 MHz and a temperature of 300 K. A standard NMR pulse sequence (recycle delay-90°-t1-90°-tm-90°-acquisition) was applied to acquire one-dimensional Proton NMR spectral data, where t1 was set to 3 μs and tm (mixing time) was set to 100 ms. Water suppression was achieved using selective irradiation during a recycle delay of 2 s and tm. A 90° pulse was adjusted to 10 μs. A total of 128 scans were collected into 64 k data points with a spectral width of 20 ppm.
For further information on sample collection and processing please see reference below. Pre-processing of raw NMR data is described in the MetaboMate vignette Data Import and Preprocessing.
Author(s)
Torben Kimhofer tkimhofer@gmail.com
Source
Dr. Jia V. Li, Imperial College London, Department of Surgery and Cancer, Centre for Computational and Systems Medicine. https://www.imperial.ac.uk/people/jia.li
References
Li, Jia V., et al. (2011) Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk. Gut. 60.9, 1214-1223.
https://www.ncbi.nlm.nih.gov/pubmed/21572120
kimsche/MetaboMate documentation built on Aug. 8, 2020, 1:14 a.m.
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Description Usage Format Details Author(s) Source References
Description
Metabolic profiling NMR dataset of murine urine samples before and after undergoing bariatric surgery (Roux-en-Y gastric bypass).
Usage
1 |
Format
A list with three elements:
- X.pqn
Matrix of pre-processed Proton NMR spectra with rows representing spectra
- ppm
Chemical shift vector in ppm with its length equals the number of columns in
X.pqn- meta
Spectrometer metadata
Details
One dimensional proton NMR spectra of murine urine samples, acquired on a Bruker Avance III spectrometer (Bruker, Rheinstetten, Germany) operating at a frequency of 600.13 MHz and a temperature of 300 K. A standard NMR pulse sequence (recycle delay-90°-t1-90°-tm-90°-acquisition) was applied to acquire one-dimensional Proton NMR spectral data, where t1 was set to 3 μs and tm (mixing time) was set to 100 ms. Water suppression was achieved using selective irradiation during a recycle delay of 2 s and tm. A 90° pulse was adjusted to 10 μs. A total of 128 scans were collected into 64 k data points with a spectral width of 20 ppm.
For further information on sample collection and processing please see reference below. Pre-processing of raw NMR data is described in the MetaboMate vignette Data Import and Preprocessing.
Author(s)
Torben Kimhofer tkimhofer@gmail.com
Source
Dr. Jia V. Li, Imperial College London, Department of Surgery and Cancer, Centre for Computational and Systems Medicine. https://www.imperial.ac.uk/people/jia.li
References
Li, Jia V., et al. (2011) Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk. Gut. 60.9, 1214-1223.
https://www.ncbi.nlm.nih.gov/pubmed/21572120
R Package Documentation
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