Summary of Study ST002385
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 PR001535. The data can be accessed directly via it's Project DOI: 10.21228/M88T5J This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
Study ID | ST002385 |
Study Title | Metabolomics in small-spotted catshark reproduction- Seminal plasma Semi-polar |
Study Summary | this study aimed to elucidate the influence of the environment (wild vs. aquarium) on the metabolic signatures in the seminal plasma (wild-captured vs. aquarium-housed). |
Institute | Universidad CEU San Pablo |
Last Name | Lorenzo Rebenaque |
First Name | Laura |
Address | Ed. Seminario. S/n, Moncada, Valencia, 46113, Spain |
laura.lorenzorebenaque@uchceu.es | |
Phone | 615056012 |
Submit Date | 2022-11-27 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2022-12-30 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001535 |
Project DOI: | doi: 10.21228/M88T5J |
Project Title: | Metabolomics in Small-spotted catshark reproduction |
Project Summary: | This study aimed to elucidate the influence of the environment (wild vs. aquarium) on the metabolic signatures in the seminal plasma and peripheral blood plasma in small-spotted catshark (wild-captured vs. aquarium-housed). |
Institute: | Universidad CEU San Pablo |
Last Name: | Lorenzo Rebenaque |
First Name: | Laura |
Address: | Ed. Seminario. S/n, Moncada, Valencia, 46113, Spain |
Email: | laura.lorenzorebenaque@uchceu.es |
Phone: | 615056012 |
Subject:
Subject ID: | SU002474 |
Subject Type: | Fish |
Subject Species: | Scyliorhinus canicula |
Species Group: | Fish |
Factors:
Subject type: Fish; Subject species: Scyliorhinus canicula (Factor headings shown in green)
mb_sample_id | local_sample_id | Group | Sample |
---|---|---|---|
SA237994 | PO6 | aquarium-housed | seminal plasma |
SA237995 | PO1 | aquarium-housed | seminal plasma |
SA237996 | PO5 | aquarium-housed | seminal plasma |
SA237997 | PO7 | aquarium-housed | seminal plasma |
SA237998 | PO2 | aquarium-housed | seminal plasma |
SA237999 | PO4 | aquarium-housed | seminal plasma |
SA238000 | PO3 | aquarium-housed | seminal plasma |
SA238001 | PS9 | wild-captured | seminal plasma |
SA238002 | PS10 | wild-captured | seminal plasma |
SA238003 | PS12 | wild-captured | seminal plasma |
SA238004 | PS8 | wild-captured | seminal plasma |
SA238005 | PS11 | wild-captured | seminal plasma |
SA238006 | PS3 | wild-captured | seminal plasma |
SA238007 | PS2 | wild-captured | seminal plasma |
SA238008 | PS1 | wild-captured | seminal plasma |
SA238009 | PS4 | wild-captured | seminal plasma |
SA238010 | PS5 | wild-captured | seminal plasma |
SA238011 | PS6 | wild-captured | seminal plasma |
SA238012 | PS7 | wild-captured | seminal plasma |
Showing results 1 to 19 of 19 |
Collection:
Collection ID: | CO002467 |
Collection Summary: | Seminal plasma samples were collected and immediately snap frozen for metabolomics analysis at the end of experiment |
Sample Type: | Seminal plasma |
Treatment:
Treatment ID: | TR002486 |
Treatment Summary: | Samples were collected from a total of 12 wild small-spotted catsharks from the Mediterranean Sea and 7 aquarium-housed small-spotted catsharks in collaboration with Oceanogràfic of Valencia. Location (wild vs. aquarium). Wild individuals were donated from local fisheries at the Valencian Community and were part of accidental captures intended to commercial fisheries ports at Valencia (39°26′45″N 0°19′12″O), Jávea (38°47′21″N 0°09′47″E) and Cullera port (39°09′58″N 0°15′10″O). Mediterranean Sea water parameters, measured by Valencia buoy (39º52′N0º20′E) were 14.6-19 °C temperature and 34-37 g/l salinity (http://www.puertos.es/es-es/oceanografia/Paginas/portus.aspx). Small-spotted catsharks under managed care were housed at Oceanogràfic of Valencia, Spain, in closed and recirculation system under controlled conditions, monitored water quality (17–21°C, 5.1 mg/l oxygen, 36 g/l salinity and 7.6–8.2 pH), fixed photoperiod (12:12 h) and disinfection using UV light and ozone. |
Sample Preparation:
Sampleprep ID: | SP002480 |
Sampleprep Summary: | Seminal plasma were subjected to a comparative metabolomics analysis. For aquarium-housed individuals’ 7 samples of both types (Seminal plasma and peripheral blood plasma), were analysed to study the semi-polar and non-polar fractions. For wild-captured individuals’ 12 samples of both types (Seminal plasma and peripheral blood plasma), were analysed to study the semi-polar and non-polar fractions. For semi-polar analysis, metabolites were extracted from 100 μL of each Seminal plasma or peripheral blood plasma samples following a published method with a little modification (Y. Yu et al., 2021). Briefly, samples were dissolved in 200 μL of cold aqueous methanol (75 %), and 200 μL of acetronitrile (75 %), spiked with 10 μg/ml formononetin as internal standard. Then, the mixture was centrifugated at 20,000 xg for 15 min at 4 °C. The supernate (200 μL) was gained, and dried under low-temperature vacuum (Thermo Scientific, USA). The samples were redissolved resuspended with 100 μL of methanol (10 %) and transferred to HPLC tubes and an aliquot of 3 μL was injected for the analysis. For no-polar analysis, metabolites were extracted from 50 μL of each Seminal plasma or peripheral blood plasma samples following a published method with a little modification (Y. Yu et al., 2021). Briefly, samples were dissolved in 300 μL of cold aqueous methanol (100 %), spiked with 50 μg/ml alpha-tocopherol acetate as internal standard. Then, the mixture was swirled for 120 seconds, and 900 μL MTBE and 250 μL ultrapure water were added. After vortexed for 15 mins, the mixture was placed 30 min at 4 ℃. Then, the supernatants (900 μL) were gained, and dried under low-temperature vacuum (Thermo Scientific, USA). The samples were redissolved resuspended with 600 μL of acetonitrile–isopropanol mixture and transferred to HPLC tubes and an aliquot of 3 μL was injected for the analysis. |
Combined analysis:
Analysis ID | AN003885 | AN003886 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
Column | Phenomenex Luna (100 x 2.1mm,2.5um) | Phenomenex Luna (100 x 2.1mm,2.5um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE | NEGATIVE |
Units | m/z ratio | m/z ratio |
Chromatography:
Chromatography ID: | CH002879 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Phenomenex Luna (100 x 2.1mm,2.5um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003625 |
Analysis ID: | AN003885 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | For the untargeted metabolomic analysis, Compound Discoverer software (Thermofisher Scientific) was used to identify the peaks, peak filtration, and peak alignment, and performed chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses (m/z). |
Ion Mode: | POSITIVE |
MS ID: | MS003626 |
Analysis ID: | AN003886 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | For the untargeted metabolomic analysis, Compound Discoverer software (Thermofisher Scientific) was used to identify the peaks, peak filtration, and peak alignment, and performed chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses (m/z). |
Ion Mode: | NEGATIVE |