Summary of Study ST002387

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	ST002387
Study Title	Metabolomics in small-spotted catshark reproduction- Blood plasma Semi-polar
Study Summary	this study aimed to elucidate the influence of the environment (wild vs. aquarium) on the metabolic signatures in the blood 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	2022-12-05
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:	SU002476
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
SA238030	SO1	aquarium-housed	blood plasma
SA238031	SO5	aquarium-housed	blood plasma
SA238032	SO6	aquarium-housed	blood plasma
SA238033	SO2	aquarium-housed	blood plasma
SA238034	SO4	aquarium-housed	blood plasma
SA238035	SO3	aquarium-housed	blood plasma
SA238036	SS8	wild-captured	blood plasma
SA238037	SS9	wild-captured	blood plasma
SA238038	SS11	wild-captured	blood plasma
SA238039	SS7	wild-captured	blood plasma
SA238040	SS10	wild-captured	blood plasma
SA238041	SS3	wild-captured	blood plasma
SA238042	SS1	wild-captured	blood plasma
SA238043	SS2	wild-captured	blood plasma
SA238044	SS4	wild-captured	blood plasma
SA238045	SS5	wild-captured	blood plasma
SA238046	SS6	wild-captured	blood plasma

Showing results 1 to 17 of 17

Showing results 1 to 17 of 17

Collection:

Collection ID:	CO002469
Collection Summary:	Blood plasma samples were collected and immediately snap frozen for metabolomics analysis at the end of experiment
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR002488
Treatment Summary:	Samples were collected from a total of 11 wild small-spotted catsharks from the Mediterranean Sea and 6 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:

TR002488

Treatment Summary:

Samples were collected from a total of 11 wild small-spotted catsharks from the Mediterranean Sea and 6 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:	SP002482
Sampleprep Summary:	Blood 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:

SP002482

Sampleprep Summary:

Blood 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	AN003889	AN003890
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:	CH002881
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Phenomenex Luna (100 x 2.1mm,2.5um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003629
Analysis ID:	AN003889
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:	MS003630
Analysis ID:	AN003890
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