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.

Show all samples  |  Perform analysis on untargeted data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data
Study IDST001494
Study TitleMetabolomics of murine embryos cultured in a microfluidic device and comparison with traditional microdrops culture
Study SummaryGlobal 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 NameMancini
First NameVanessa
AddressWoodhouse Lane, Leeds, LS29JT
Emailelvm@leeds.ac.uk
Phone+447599197366
Submit Date2020-08-29
Analysis Type DetailLC-MS
Release Date2020-10-13
Release Version1
Vanessa Mancini Vanessa Mancini
https://dx.doi.org/10.21228/M8W99G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA125932SC_20190605_RPLCp_FMS_Embryo_S1bControl_device
SA125933SC_20190605_RPLCp_FMS_Embryo_S3bControl_device
SA125934SC_20190605_RPLCp_FMS_Embryo_S2bControl_device
SA125935SC_20191202_FMS_Embryo_S02_T1Control_drops
SA125936SC_20191202_FMS_Embryo_S03_T1Control_drops
SA125937SC_20191202_FMS_Embryo_S01_T2Control_drops
SA125938SC_20190605_RPLCp_FMS_Embryo_S14Embryo culture media_device
SA125939SC_20190605_RPLCp_FMS_Embryo_S13Embryo culture media_device
SA125940SC_20190605_RPLCp_FMS_Embryo_S15Embryo culture media_device
SA125941SC_20191202_FMS_Embryo_S14_T2Embryo culture media_drops
SA125942SC_20191202_FMS_Embryo_S13_T1Embryo culture media_drops
SA125943SC_20191202_FMS_Embryo_S15_T1Embryo culture media_drops
SA125944SC_20190605_RPLCp_FMS_Embryo_S8No embryos_device
SA125945SC_20190605_RPLCp_FMS_Embryo_S9No embryos_device
SA125946SC_20190605_RPLCp_FMS_Embryo_S7No embryos_device
SA125947SC_20191202_FMS_Embryo_S07_T1No embryos_drops
SA125948SC_20191202_FMS_Embryo_S08_T1No embryos_drops
SA125949SC_20191202_FMS_Embryo_S09_T2No embryos_drops
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.

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 (1.9 µm, 2.1mm x 100 mm) Thermo Hypersil Gold (1.9 µm, 2.1mm x 100 mm)
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 (1.9 µm, 2.1mm x 100 mm)
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
  logo