Summary of Study ST002030

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 PR001287. The data can be accessed directly via it's Project DOI: 10.21228/M8BX22 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.

Study ID	ST002030
Study Title	Metabolomics Analysis of Blood Plasma and Stool from Six Week Flaxseed Dietary Intervention in Postmenopausal Women (Stool/Bile acids)
Study Summary	Samples were taken before and after 6 weeks of flaxseed dietary intervention. Serum and fecal metabolomics were performed to characterize the metabolomic profiles of serum and stool metabolites pre- and post-intervention.
Institute	University of California, Davis
Last Name	folz
First Name	jake
Address	451 Health Science Drive
Email	jfolz@ucdavis.edu
Phone	7155636311
Submit Date	2021-12-21
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	LC-MS
Release Date	2023-01-02
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001287
Project DOI:	doi: 10.21228/M8BX22
Project Title:	Metabolomics Analysis of Blood Plasma and Stool from Six Week Flaxseed Dietary Intervention in Postmenopausal Women
Project Summary:	Samples were taken before and after 6 weeks of flaxseed dietary intervention. Serum and fecal metabolomics were performed to characterize the metabolomic profiles of serum and stool metabolites pre- and post-intervention.
Institute:	University of California, Davis
Last Name:	Folz
First Name:	jake
Address:	451 Health Science Drive
Email:	jfolz@ucdavis.edu
Phone:	7155636311

Subject:

Subject ID:	SU002112
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA191107	RS-01920609	Post-intervention
SA191108	RS-01916436	Post-intervention
SA191109	RS-02219083	Post-intervention
SA191110	RS-02217669	Post-intervention
SA191111	RS-01912456	Post-intervention
SA191112	RS-01923384	Post-intervention
SA191113	RS-01940439	Post-intervention
SA191114	RS-01933527	Post-intervention
SA191115	RS-02210756	Post-intervention
SA191116	RS-01909498	Post-intervention
SA191117	RS-02220151	Post-intervention
SA191118	RS-02254825	Post-intervention
SA191119	RS-02269483	Post-intervention
SA191120	RS-01865119	Post-intervention
SA191121	RS-01851707	Post-intervention
SA191122	RS-02248450	Post-intervention
SA191123	RS-01891737	Post-intervention
SA191124	RS-01950714	Post-intervention
SA191125	RS-02221392	Post-intervention
SA191126	RS-01899167	Post-intervention
SA191127	RS-01906962	Post-intervention
SA191128	RS-02209055	Post-intervention
SA191129	RS-02177788	Post-intervention
SA191130	RS-02099628	Post-intervention
SA191131	RS-02097213	Post-intervention
SA191132	RS-02179395	Post-intervention
SA191133	RS-02119956	Post-intervention
SA191134	RS-02129908	Post-intervention
SA191135	RS-02139810	Post-intervention
SA191136	RS-02136575	Post-intervention
SA191137	RS-02135615	Post-intervention
SA191138	RS-02186686	Post-intervention
SA191139	RS-02055701	Post-intervention
SA191140	RS-02207959	Post-intervention
SA191141	RS-02208413	Post-intervention
SA191142	RS-01975227	Post-intervention
SA191143	RS-02019533	Post-intervention
SA191144	RS-02193478	Post-intervention
SA191145	RS-02055250	Post-intervention
SA191146	RS-02045482	Post-intervention
SA191147	RS-02040176	Post-intervention
SA191148	RS-01838033	Post-intervention
SA191149	RS-01871547	Post-intervention
SA191150	RS-02622760	Post-intervention
SA191151	RS-01713712	Post-intervention
SA191152	RS-01707130	Post-intervention
SA191153	RS-01704567	Post-intervention
SA191154	RS-02309902	Post-intervention
SA191155	RS-02621442	Post-intervention
SA191156	RS-01735982	Post-intervention
SA191157	RS-01730343	Post-intervention
SA191158	RS-02583618	Post-intervention
SA191159	RS-02637716	Post-intervention
SA191160	RS-01694989	Post-intervention
SA191161	RS-01607340	Post-intervention
SA191162	RS-02756031	Post-intervention
SA191163	RS-01586115	Post-intervention
SA191164	RS-01574184	Post-intervention
SA191165	RS-01617214	Post-intervention
SA191166	RS-02750185	Post-intervention
SA191167	RS-02674498	Post-intervention
SA191168	RS-01686993	Post-intervention
SA191169	RS-01648850	Post-intervention
SA191170	RS-02354063	Post-intervention
SA191171	RS-01718537	Post-intervention
SA191172	RS-01776131	Post-intervention
SA191173	RS-01775777	Post-intervention
SA191174	RS-01747171	Post-intervention
SA191175	RS-01807614	Post-intervention
SA191176	RS-01830763	Post-intervention
SA191177	RS-01770486	Post-intervention
SA191178	RS-01803066	Post-intervention
SA191179	RS-01759730	Post-intervention
SA191180	RS-01764367	Post-intervention
SA191181	RS-02159560	Pre-intervention
SA191182	RS-02173570	Pre-intervention
SA191183	RS-02174019	Pre-intervention
SA191184	RS-02176985	Pre-intervention
SA191185	RS-02343753	Pre-intervention
SA191186	RS-02328916	Pre-intervention
SA191187	RS-02281190	Pre-intervention
SA191188	RS-02163124	Pre-intervention
SA191189	RS-02171917	Pre-intervention
SA191190	RS-02282708	Pre-intervention
SA191191	RS-02734868	Pre-intervention
SA191192	RS-02505149	Pre-intervention
SA191193	RS-02349304	Pre-intervention
SA191194	RS-02186695	Pre-intervention
SA191195	RS-02232959	Pre-intervention
SA191196	RS-02189596	Pre-intervention
SA191197	RS-02224703	Pre-intervention
SA191198	RS-02636728	Pre-intervention
SA191199	RS-02245717	Pre-intervention
SA191200	RS-02348498	Pre-intervention
SA191201	RS-02348451	Pre-intervention
SA191202	RS-02184855	Pre-intervention
SA191203	RS-02724295	Pre-intervention
SA191204	RS-02681370	Pre-intervention
SA191205	RS-02731752	Pre-intervention
SA191206	RS-01975879	Pre-intervention

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Collection:

Collection ID:	CO002105
Collection Summary:	Samples were taken before and after 6 weeks of flaxseed dietary intervention. Serum and fecal metabolomics were performed to characterize the metabolomic profiles of serum and stool metabolites pre- and post-intervention.
Sample Type:	Feces

Treatment:

Treatment ID:	TR002124
Treatment Summary:	Samples were taken before and after 6 weeks of flaxseed dietary intervention. Serum and fecal metabolomics were performed to characterize the metabolomic profiles of serum and stool metabolites pre- and post-intervention.

Sample Preparation:

Sampleprep ID:	SP002118
Sampleprep Summary:	Different procedures have to be used for different sample matrices; this SOP focuses mainly on bile acids in blood plasma but includes other current protocols 5.1. Isolation of an enriched bile acid fraction from blood plasma or serum • Prepare a plate map showing location of samples in wells. Include wells with method blanks and controls on each plate. • Per well add 50µL plasma sample (excluding Method Blanks, IS Check and Utak Controls) -Method Blanks: Contains Anti-Oxidant Solution, CUDA/PHAU in MeOH:ACN Final Vol 250uL -IS Check: Contains Anti-Oxidant Solution, SSTD, CUDA/PHAU in MeOH:ACN Final Vol 250uL -Utak Controls: Conatins 50uL Utak Serum, Anti-Oxidant Sol, SSTD, CUDA/PAHU in MeOH:ACN Final Vol 250uL ● To each well, add 25 µL Anti-Oxidant Solution ● To each IS Check, Utak Control and Customer Sample, add 25 µL SSTD (Final Volume 100nM) ● To each well, add 25 µL CUDA/PHAU (Final Volume 100nM) ● Add 50:50 MeOH:ACN to each well for a final volume of 250uL.Cap or seal plate with Silicon or Foil Mat and vortex for 1 minute at speed 7. ● Centrifuge plate for 5 minutes so protein precipitates into firm pellet at the bottom of each well ● Pipette roughly 200uL of supernatant into 96 Well PVDF Filter Plate with additional 96 Well Nunc Sample plate ● Centrifuge PVDF Filter plate containing samples into collection plate ● Cover plate with Silicon Nunc Plug mat if plate is being stored at -20C, Cover with Pre-Slit Mat for LC-MS Analysis 5.2. Isolation of an enriched bile acid fraction from tissue, e.g. liver or spinal cord ● Weigh tissue sample into eppendorf tube (amount depending on bile acid content) ● Add 10uL Anti-Oxidant Solution (0.2 mg/ml solution BHT/EDTA in 1:1 methanol/water) use repeater pipetter or syringe repeater assembly. ● Add 10uL SSTD 1000nM Solution, use repeater pipetter or syringe repeater assembly ● Add 500uL Cold MeOH and 2 steel balls (3 mm diameter) and homogenize with GenoGrinder in two 30 sec intervals at 1500 rpm until a fine suspension is achieved. ● Centrifuge at 2C for 3 minutes spinning at 15,000rcf. Transfer methanol supernatant to 1.5 mL eppendorf vial containing 10uL 20% glycerol solution ● Add 500uL Cold MeOH and repeat homogenization with GenoGrinder in two 30 sec intervals at 1500 rpm until a fine suspension is achieved. Centrifuge again and add to the same 1.5mL tube ● Evaporated to dryness, or if a large number of samples has to be processed to a 96-well plate ● Re-suspend pellet in 100uL CUDA/PHAU 100nM MeOH:ACN ● Shake reconstitution for 1 minute at speed of 7 and let stand on wet ice for 15 minutes protected from light ● Shake reconstitution again and filter using PVDF Filter plate or Durapore Spin Filters. ● Transfer filtrate to glass insert in amber vial and cap or 96 well plate with pre-slit silicon mat ● Store at -20°C until LCMS analysis 5.3. Isolation of an enriched bile acid fraction from fecal water ● Label eppendorf tubes; add additional vials for blanks and controls ● Add 10uL Anti-Oxidant Solution using repeater pipetter or syringe repeater assembly ● Add 10uL SSTD using repeater pipetter or syringe repeater assembly ● Thaw out samples of fecal water, vortex briefly to homogenize, keep on ice ● Pipette 10uL of fecal water sample into labeled vials. ● Add 800uL of cold extraction solvent, acetonitrile containing 5% of ammonia ● Vortex samples, then shake for 6 minutes at 4 degree C ● Centrifuge for 3 minutes ● Transfer supernatant to fresh 1.5 mL eppendorf vials and evaporated to dryness, or for a large number of samples, to a 96-well plate and discard centrifugation residues ● Add 100µL CUDA/PHAU IS 100nM to dried sample, cap and vortex 10 sec to dissolve residues ● Set rack of samples on wet ice for 15min ● Filter using PVDF Plate or individual Spin Filters ● Transfer filtrates to glass insert in amber vial and cap or to 96 Well Plate ● Store at -20°C until LCMS analysis

Sampleprep ID:

SP002118

Sampleprep Summary:

Different procedures have to be used for different sample matrices; this SOP focuses mainly on bile acids in blood plasma but includes other current protocols 5.1. Isolation of an enriched bile acid fraction from blood plasma or serum • Prepare a plate map showing location of samples in wells. Include wells with method blanks and controls on each plate. • Per well add 50µL plasma sample (excluding Method Blanks, IS Check and Utak Controls) -Method Blanks: Contains Anti-Oxidant Solution, CUDA/PHAU in MeOH:ACN Final Vol 250uL -IS Check: Contains Anti-Oxidant Solution, SSTD, CUDA/PHAU in MeOH:ACN Final Vol 250uL -Utak Controls: Conatins 50uL Utak Serum, Anti-Oxidant Sol, SSTD, CUDA/PAHU in MeOH:ACN Final Vol 250uL ● To each well, add 25 µL Anti-Oxidant Solution ● To each IS Check, Utak Control and Customer Sample, add 25 µL SSTD (Final Volume 100nM) ● To each well, add 25 µL CUDA/PHAU (Final Volume 100nM) ● Add 50:50 MeOH:ACN to each well for a final volume of 250uL.Cap or seal plate with Silicon or Foil Mat and vortex for 1 minute at speed 7. ● Centrifuge plate for 5 minutes so protein precipitates into firm pellet at the bottom of each well ● Pipette roughly 200uL of supernatant into 96 Well PVDF Filter Plate with additional 96 Well Nunc Sample plate ● Centrifuge PVDF Filter plate containing samples into collection plate ● Cover plate with Silicon Nunc Plug mat if plate is being stored at -20C, Cover with Pre-Slit Mat for LC-MS Analysis 5.2. Isolation of an enriched bile acid fraction from tissue, e.g. liver or spinal cord ● Weigh tissue sample into eppendorf tube (amount depending on bile acid content) ● Add 10uL Anti-Oxidant Solution (0.2 mg/ml solution BHT/EDTA in 1:1 methanol/water) use repeater pipetter or syringe repeater assembly. ● Add 10uL SSTD 1000nM Solution, use repeater pipetter or syringe repeater assembly ● Add 500uL Cold MeOH and 2 steel balls (3 mm diameter) and homogenize with GenoGrinder in two 30 sec intervals at 1500 rpm until a fine suspension is achieved. ● Centrifuge at 2C for 3 minutes spinning at 15,000rcf. Transfer methanol supernatant to 1.5 mL eppendorf vial containing 10uL 20% glycerol solution ● Add 500uL Cold MeOH and repeat homogenization with GenoGrinder in two 30 sec intervals at 1500 rpm until a fine suspension is achieved. Centrifuge again and add to the same 1.5mL tube ● Evaporated to dryness, or if a large number of samples has to be processed to a 96-well plate ● Re-suspend pellet in 100uL CUDA/PHAU 100nM MeOH:ACN ● Shake reconstitution for 1 minute at speed of 7 and let stand on wet ice for 15 minutes protected from light ● Shake reconstitution again and filter using PVDF Filter plate or Durapore Spin Filters. ● Transfer filtrate to glass insert in amber vial and cap or 96 well plate with pre-slit silicon mat ● Store at -20°C until LCMS analysis 5.3. Isolation of an enriched bile acid fraction from fecal water ● Label eppendorf tubes; add additional vials for blanks and controls ● Add 10uL Anti-Oxidant Solution using repeater pipetter or syringe repeater assembly ● Add 10uL SSTD using repeater pipetter or syringe repeater assembly ● Thaw out samples of fecal water, vortex briefly to homogenize, keep on ice ● Pipette 10uL of fecal water sample into labeled vials. ● Add 800uL of cold extraction solvent, acetonitrile containing 5% of ammonia ● Vortex samples, then shake for 6 minutes at 4 degree C ● Centrifuge for 3 minutes ● Transfer supernatant to fresh 1.5 mL eppendorf vials and evaporated to dryness, or for a large number of samples, to a 96-well plate and discard centrifugation residues ● Add 100µL CUDA/PHAU IS 100nM to dried sample, cap and vortex 10 sec to dissolve residues ● Set rack of samples on wet ice for 15min ● Filter using PVDF Plate or individual Spin Filters ● Transfer filtrates to glass insert in amber vial and cap or to 96 Well Plate ● Store at -20°C until LCMS analysis

Combined analysis:

Analysis ID	AN003300
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Vanquish
Column	Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type	ESI
MS instrument type	Ion trap
MS instrument name	ABI Sciex 6500+
Ion Mode	NEGATIVE
Units	pg/mg wet stool

Chromatography:

Chromatography ID:	CH002439
Instrument Name:	Vanquish
Column Name:	Waters Acquity BEH C18 (100 x 2mm,1.7um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003070
Analysis ID:	AN003300
Instrument Name:	ABI Sciex 6500+
Instrument Type:	Ion trap
MS Type:	ESI
MS Comments:	Extracts were analyzed by liquid chromatography (Waters ACQUITY UPLC I-Class system) coupled to a Sciex 6500+ QTRAP hybrid, triple quadrupole linear ion trap mass spectrometer. 5 µL of each extract was injected. Scheduled multiple reaction monitoring (MRM) was performed with optimized collision energies, de-clustering potentials, and collision cell exit potentials for individual analyte. A LC-MRM targeted method was used to analyze both bile acids and steroids with positive and negative polarity switching. Oxylipins were analyzed in another LC-MRM method in negative ionization mode only. All analytes were quantified against 6-point calibration curves using internal standards. Turbo Spray Ion Source parameters are: curtain gas (CUR) 25 psi, nebulizer gas (GS1) 50 psi, turbo-gas (GS2) 50 psi, electrospray voltage −4.5 kV/+3 kV, and source temperature 525 ◦C. Nitrogen was used as the collision gas. Software Analyst 1.6.3 and MultiQuant 3.0.2 (AB Sciex) were used for data acquisition and quantification. MRM transitions for the analytes are provided in the supplementary Tables S8 and S9
Ion Mode:	NEGATIVE