Summary of Study ST001494

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 PR001012. The data can be accessed directly via it's Project DOI: 10.21228/M8W99G 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	ST001494
Study Title	Metabolomics of murine embryos cultured in a microfluidic device and comparison with traditional microdrops culture
Study Summary	Global untargeted metabolomics study to analyse culture media extracted from an innovative microfluidic device or traditional microdrops in presence or absence of murine embryos to investigate PDMS-release of biomolecules and embryo metabolic activity.
Institute	University of Leeds
Last Name	Mancini
First Name	Vanessa
Address	Woodhouse Lane, Leeds, LS29JT
Email	elvm@leeds.ac.uk
Phone	+447599197366
Submit Date	2020-08-29
Analysis Type Detail	LC-MS
Release Date	2020-10-13
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001012
Project DOI:	doi: 10.21228/M8W99G
Project Title:	Embryo device MS study
Project Summary:	Metabolomics study of murine embryos cultured in an innovative microfluidic device to assess release of plastic-related compounds and embryo metabolic activity.
Institute:	University of Leeds
Department:	Electronic and Electrical Engineering
Laboratory:	Bioelectronics Lab
Last Name:	Mancini
First Name:	Vanessa
Address:	Woodhouse Lane, Leeds, West Yorkshire, LS62HN, United Kingdom
Email:	elvm@leeds.ac.uk
Phone:	+447599197366

Subject:

Subject ID:	SU001568
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Device
SA125932	SC_20190605_RPLCp_FMS_Embryo_S1b	Control_device
SA125933	SC_20190605_RPLCp_FMS_Embryo_S3b	Control_device
SA125934	SC_20190605_RPLCp_FMS_Embryo_S2b	Control_device
SA125935	SC_20191202_FMS_Embryo_S02_T1	Control_drops
SA125936	SC_20191202_FMS_Embryo_S03_T1	Control_drops
SA125937	SC_20191202_FMS_Embryo_S01_T2	Control_drops
SA125938	SC_20190605_RPLCp_FMS_Embryo_S14	Embryo culture media_device
SA125939	SC_20190605_RPLCp_FMS_Embryo_S13	Embryo culture media_device
SA125940	SC_20190605_RPLCp_FMS_Embryo_S15	Embryo culture media_device
SA125941	SC_20191202_FMS_Embryo_S14_T2	Embryo culture media_drops
SA125942	SC_20191202_FMS_Embryo_S13_T1	Embryo culture media_drops
SA125943	SC_20191202_FMS_Embryo_S15_T1	Embryo culture media_drops
SA125944	SC_20190605_RPLCp_FMS_Embryo_S8	No embryos_device
SA125945	SC_20190605_RPLCp_FMS_Embryo_S9	No embryos_device
SA125946	SC_20190605_RPLCp_FMS_Embryo_S7	No embryos_device
SA125947	SC_20191202_FMS_Embryo_S07_T1	No embryos_drops
SA125948	SC_20191202_FMS_Embryo_S08_T1	No embryos_drops
SA125949	SC_20191202_FMS_Embryo_S09_T2	No embryos_drops

Showing results 1 to 18 of 18

Showing results 1 to 18 of 18

Collection:

Collection ID:	CO001563
Collection Summary:	Samples were collected from microdrops and microfluidic devices when embryos developed to fully expanded blastocyst stage, to allow stage-matched comparison of embryo metabolite production/consumption.
Sample Type:	Blastocysts

Treatment:

Treatment ID:	TR001583
Treatment Summary:	Control KSOM: fresh medium at day 0 not incubated in devices or microdrops. Day 4 KSOM_drop: medium incubated in microdrops for 4 days without embryos Day 5 KSOM_device: medium incubated in devices for 5 days without embryos Day 4 KSOM_drop_embryos: medium incubated in microdrops for 4 days with embryos Day 5 KSOM_device_embryos: medium incubated in devices for 5 days with embryos

Sample Preparation:

Sampleprep ID:	SP001576
Sampleprep Summary:	Culture media samples (100 µl) were thawed on ice and prepared using previously described methods. Briefly, 300 µL of dry ice cooled methanol was added to individual culture medium samples and incubated overnight at -80°C; individual samples were spun down to remove proteins and subsequent supernatant used for analyses. Samples were separated and analysed using reverse-phase liquid chromatography connected to a a Thermo Scientific Q Exactive HF (LC-Hybrid Quadrupole-Orbitrap MS/MS) instrument using positive ion mode MS.

Sampleprep ID:

SP001576

Sampleprep Summary:

Culture media samples (100 µl) were thawed on ice and prepared using previously described methods. Briefly, 300 µL of dry ice cooled methanol was added to individual culture medium samples and incubated overnight at -80°C; individual samples were spun down to remove proteins and subsequent supernatant used for analyses. Samples were separated and analysed using reverse-phase liquid chromatography connected to a a Thermo Scientific Q Exactive HF (LC-Hybrid Quadrupole-Orbitrap MS/MS) instrument using positive ion mode MS.

Combined analysis:

Analysis ID	AN002476	AN002477
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Thermo Hypersil Gold (100 x 2.1mm,1.9um)	Thermo Hypersil Gold (100 x 2.1mm,1.9um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive HF hybrid Orbitrap	Thermo Q Exactive HF hybrid Orbitrap
Ion Mode	POSITIVE	POSITIVE
Units	peak area	peak area

Chromatography:

Chromatography ID:	CH001814
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Hypersil Gold (100 x 2.1mm,1.9um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002296
Analysis ID:	AN002476
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Full MS analyses were acquired over a mass range of m/z 70-1050 under an ESI positive profile mode. Full mass scan was used at a resolution of 120,000 with a scan rate at ∼3.5 Hz Raw data were imported, processed, normalized, and reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK). All FMS sample runs were aligned against a FMS QC pool reference, with alignment to the reference being ≥ 96%, demonstrating the reproducibility of the RPLC column separation method. Peak picking, with a minimum threshold of 100,000 ion intensity, was performed for individual aligned runs based on an aggregate run (representative of all ion peaks detected in all samples).
Ion Mode:	POSITIVE

MS ID:	MS002297
Analysis ID:	AN002477
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Full MS analyses were acquired over a mass range of m/z 70-1050 under an ESI positive profile mode. Full mass scan was used at a resolution of 120,000 with a scan rate at ∼3.5 Hz Raw data were imported, processed, normalized, and reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK). All FMS sample runs were aligned against a FMS QC pool reference, with alignment to the reference being ≥ 96%, demonstrating the reproducibility of the RPLC column separation method. Peak picking, with a minimum threshold of 100,000 ion intensity, was performed for individual aligned runs based on an aggregate run (representative of all ion peaks detected in all samples).
Ion Mode:	POSITIVE