Summary of study ST001088

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 PR000727. The data can be accessed directly via it's Project DOI: 10.21228/M8Q38G This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Download all metabolite data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data (Contains raw data)
Study IDST001088
Study TitlePhysiological and metabolic response of crab megalopae and juveniles to ocean acidification (part-I)
Study SummaryThe objective of the study was to examine the physiological and metabolic response of crab megalopae and juveniles to ocean acidification treatment. Four treatments were used:high pH, high DO (dissolved oxygen); high pH, low DO; low pH, high DO; low pH, low DO
Institute
NOAA NWFSC
DepartmentCB Division
Last NameNichols
First NameKrista
Address1315 East-West Highway Silver Spring, MD 20910
Emailkrista.nichols@noaa.gov
Phone206-302-2470
Submit Date2018-10-15
Num Groups4
Total Subjects60
Raw Data AvailableYes
Raw Data File Type(s).cdf
Analysis Type DetailGC-MS
Release Date2018-12-11
Release Version1
Krista Nichols Krista Nichols
https://dx.doi.org/10.21228/M8Q38G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000727
Project DOI:doi: 10.21228/M8Q38G
Project Title:GC analysis of crab megalopae and juveniles in response to ocean acidification
Project Summary:The objective of the study was to examine the physiological and metabolic response of crab megalopae and juveniles to ocean acidification treatment.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258

Subject:

Subject ID:SU001132
Subject Type:Invertebrate
Subject Species:Metacarcinus magister
Taxonomy ID:29965

Factors:

Subject type: Invertebrate; Subject species: Metacarcinus magister (Factor headings shown in green)

mb_sample_id local_sample_id TreatmentDuration (days) ph treatment DO treatment
SA073506M7C630 high high
SA073507M5B230 high high
SA073508M5D730 high high
SA073509M5B330 high high
SA073510M10C530 high low
SA073511M11C230 high low
SA073512M3A730 low high
SA073513M2C130 low high
SA073514M2B630 low high
SA073515M2B330 low high
SA073516M6A630 low low
SA073517M12A131 high high
SA073518M8D231 high high
SA073519M12A1_231 high high
SA073520M8B231 high high
SA073521M7D631 high high
SA073522M4D531 high low
SA073523M4B131 high low
SA073524M11A231 high low
SA073525M10D231 high low
SA073526M2C631 low high
SA073527M2A131 low high
SA073528M3D531 low high
SA073529M3B231 low high
SA073530M3A231 low high
SA073531M3C331 low high
SA073532M2B431 low high
SA073533M6C331 low low
SA073534M1C231 low low
SA073535M6B331 low low
SA073536M6D231 low low
SA073537M1C431 low low
SA073538M1C131 low low
SA073539M12D332 high high
SA073540M7D532 high high
SA073541M12B332 high high
SA073542M11A732 high low
SA073543M11D332 high low
SA073544M10D332 high low
SA073545M10A732 high low
SA073546M10B532 high low
SA073547M10A7_232 high low
SA073548M2B732 low high
SA073549M3D632 low high
SA073550M2C432 low high
SA073551M1B232 low low
SA073552M1C532 low low
SA073553M1A132 low low
SA073554M6A532 low low
SA073555M12B433 high high
SA073556M7A533 high high
SA073557M8C133 high high
SA073558M11B2_233 high low
SA073559M4D433 high low
SA073560M11B233 high low
SA073561M2A333 low high
SA073562M1D733 low low
SA073563M6B633 low low
SA073564M6C233 low low
SA073565M1D133 low low
Showing results 1 to 60 of 60

Collection:

Collection ID:CO001126
Collection Summary:After completing the required treatment time of 30-33 days, each crab was frozen at -80C and shipped to the West Coast Metabolomics Center.
Sample Type:Muscle Tissue

Treatment:

Treatment ID:TR001146
Treatment Summary:Four treatments were used:high pH, high DO (dissolved oxygen); high pH, low DO; low pH, high DO; low pH, low DO.

Sample Preparation:

Sampleprep ID:SP001139
Sampleprep Summary:Crabs were removed from -80°C. 15 mg of muscle tissue was removed from each crab and placed in a 2 mL eppendorph tube. 2 x 3mm grinding beads were added to each sample. 225 µL of methanol with quality control standards were added to each sample. Samples were ground for 30 seconds at 1500 rpm using a GenoGrinder. 750 µL of methyl-tertbutyl ether (MTBE) was added to each sample. Samples were vortexed for 10 seconds and then shaked at 4°C for 6 minutes. 188 µL of LC-MS grade water was added to each sample. Samples were vortexed for 10 seconds and then centrifuged for 2 minutes at 14,000 rcf. The top, organic layer was split into two 350 µL aliquots, one submitted to lipidomics analysis and one saved for backup. The bottom layer was split into two 125 µL aliquots, one submitted to GC analysis and one saved as a backup.

Combined analysis:

Analysis ID AN001773
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus HT TOF
Ion Mode POSITIVE
Units Peak Height

Chromatography:

Chromatography ID:CH001253
Instrument Name:Agilent 7890A
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Column Temperature:50-330
Flow Rate:1 mL/min
Injection Temperature:50°C ramped to 250°C by 12°C s-1
Sample Injection:0.5 uL
Oven Temperature:50°C for 1 min, then ramped at 20°C min-1 to 330°C, held constant for 5 min
Chromatography Type:GC

MS:

MS ID:MS001639
Analysis ID:AN001773
Instrument Name:Leco Pegasus HT TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Mode:POSITIVE
Ion Source Temperature:250°C
Ionization Energy:-70 eV
Dataformat:.peg, .txt, .cdf
Resolution Setting:17 spectra/sec
Scanning Range:80-500 Da
  logo