Summary of Study ST001102

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

Study ID	ST001102
Study Title	Physiological and metabolic response of crab megalopae and juveniles to ocean acidification (part-II)
Study Summary	Young crab samples were placed into 1 of 4 treatment groups to understand their metabolic response to ocean acidification and dissolved oxygen content.
Institute	NOAA NWFSC
Department	CB Division
Last Name	Nichols
First Name	Krista
Address	N/A
Email	krista.nichols@noaa.gov
Phone	206-302-2470
Submit Date	2018-11-29
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2019-01-22
Release Version	1

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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:	SU001146
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	ph treatment	DO treatment	Treatment Duration (days)
SA075065	M5D7_24	High	High	30
SA075066	M7C6_26	High	High	30
SA075067	M5B2_1	High	High	30
SA075068	M5B3_25	High	High	30
SA075069	M12A1_28	High	High	31
SA075070	M8B2_8	High	High	31
SA075071	M8D2_29	High	High	31
SA075072	M12A1_46	High	High	31
SA075073	M7D6_30	High	High	31
SA075074	M12B3_53	High	High	32
SA075075	M7D5_54	High	High	32
SA075076	M12D3_34	High	High	32
SA075077	M7A5_42	High	High	33
SA075078	M8C1_58	High	High	33
SA075079	M12B4_59	High	High	33
SA075080	M11C2_2	High	Low	30
SA075081	M10C5_27	High	Low	30
SA075082	M10D2_47	High	Low	31
SA075083	M4B1_9	High	Low	31
SA075084	M4D5_49	High	Low	31
SA075085	M11A2_48	High	Low	31
SA075086	M10B5_35	High	Low	32
SA075087	M10A7_17	High	Low	32
SA075088	M11A7_60	High	Low	32
SA075089	M10A7_43	High	Low	32
SA075090	M10D3_56	High	Low	32
SA075091	M11D3_55	High	Low	32
SA075092	M4D4_38	High	Low	33
SA075093	M11B2_22	High	Low	33
SA075094	M11B2_44	High	Low	33
SA075095	M2B3_5	Low	High	30
SA075096	M2C1_6	Low	High	30
SA075097	M2B6_4	Low	High	30
SA075098	M3A7_3	Low	High	30
SA075099	M2C6_50	Low	High	31
SA075100	M2A1_51	Low	High	31
SA075101	M3D5_31	Low	High	31
SA075102	M3A2_12	Low	High	31
SA075103	M3B2_11	Low	High	31
SA075104	M3C3_10	Low	High	31
SA075105	M2B4_13	Low	High	31
SA075106	M2B7_57	Low	High	32
SA075107	M2C4_36	Low	High	32
SA075108	M3D6_37	Low	High	32
SA075109	M2A3_23	Low	High	33
SA075110	M6A6_7	Low	Low	30
SA075111	M1C1_16	Low	Low	31
SA075112	M1C2_14	Low	Low	31
SA075113	M6C3_52	Low	Low	31
SA075114	M1C4_32	Low	Low	31
SA075115	M6D2_33	Low	Low	31
SA075116	M6B3_15	Low	Low	31
SA075117	M1A1_19	Low	Low	32
SA075118	M6A5_18	Low	Low	32
SA075119	M1B2_20	Low	Low	32
SA075120	M1C5_21	Low	Low	32
SA075121	M6C2_40	Low	Low	33
SA075122	M1D1_41	Low	Low	33
SA075123	M6B6_45	Low	Low	33
SA075124	M1D7_39	Low	Low	33

Showing results 1 to 60 of 60

Showing results 1 to 60 of 60

Collection:

Collection ID:	CO001140
Collection Summary:	After each crab completed the treatment for the predetermined length of time, crabs were frozen whole specimen at -80°C and shipped to the West Coast Metabolomics Center.
Sample Type:	Whole Animal

Treatment:

Treatment ID:	TR001160
Treatment Summary:	15 crabs were placed into 1 of 4 treatment groups: High pH:High Dissolved Oxygen, High pH:Low Dissolved Oxygen, Low pH:Low Dissolved Oxygen, Low pH: High Dissolved Oxygen. Crabs were subjected to their treatment group for 30-33 days.

Sample Preparation:

Sampleprep ID:	SP001153
Sampleprep Summary:	15mg of whole crab was placed into a 1.5mL ependorph tube. 2 x 3mm grinding beads were added to each sample. 225 µL of cold MeOH with quality controls was added to each samples. Batches of samples were ground with GenoGrinder for 30 seconds at 1500 rpm. 750µL of methyl tert-butyl Ether (MTBE) was added to each sample. Samples were vortexed for 10 seconds and then shaken at 4°C for 5 minutes using an Orbital Mixer. 188 uL of LC-MS grade water was added to each sample. Vortex for 10 seconds and then centrifuged for 2 minutes at 14,000 rcf. 2 x 350µL aliquots were removed from the top, organic layer, one submitted for analysis and the other stored as backup in -20°C. 2 x 125µL aliquots were removed from the bottom, polar layer, one submitted for analysis, the other stored at -20°C for backup.

Sampleprep ID:

SP001153

Sampleprep Summary:

15mg of whole crab was placed into a 1.5mL ependorph tube. 2 x 3mm grinding beads were added to each sample. 225 µL of cold MeOH with quality controls was added to each samples. Batches of samples were ground with GenoGrinder for 30 seconds at 1500 rpm. 750µL of methyl tert-butyl Ether (MTBE) was added to each sample. Samples were vortexed for 10 seconds and then shaken at 4°C for 5 minutes using an Orbital Mixer. 188 uL of LC-MS grade water was added to each sample. Vortex for 10 seconds and then centrifuged for 2 minutes at 14,000 rcf. 2 x 350µL aliquots were removed from the top, organic layer, one submitted for analysis and the other stored as backup in -20°C. 2 x 125µL aliquots were removed from the bottom, polar layer, one submitted for analysis, the other stored at -20°C for backup.

Combined analysis:

Analysis ID	AN001791	AN001792
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Agilent 1290	Agilent 1290
Column	Waters Acquity CSH C18 (100 x 2.1mm,1.7um)	Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Agilent 6530 QTOF	Agilent 6530 QTOF
Ion Mode	POSITIVE	NEGATIVE
Units	Peak Height	Peak Height

Chromatography:

Chromatography ID:	CH001265
Instrument Name:	Agilent 1290
Column Name:	Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Pressure:	500-1000bar
Column Temperature:	65°C
Flow Rate:	600µL/min
Sample Injection:	1.67µL
Chromatography Type:	Reversed phase

MS:

MS ID:	MS001653
Analysis ID:	AN001791
Instrument Name:	Agilent 6530 QTOF
Instrument Type:	QTOF
MS Type:	ESI
Ion Mode:	POSITIVE

MS ID:	MS001654
Analysis ID:	AN001792
Instrument Name:	Agilent 6530 QTOF
Instrument Type:	QTOF
MS Type:	ESI
Ion Mode:	NEGATIVE