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.

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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
Email	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

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

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.

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.

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