Summary of Study ST001336

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 PR000900. The data can be accessed directly via it's Project DOI: 10.21228/M8BX09 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001336
Study TitleEffect of high-fat diet and bile acid treatment on serum and tissue lipidomes in mice
Study SummaryWe analyzed mouse serum and esophageal tissue samples from a mouse dietary intervention experiment. Briefly, C57BL/6 mice (n=44) were divided into 4 groups (n=11 per group) and fed High-fat diet (HFD), 0.2% deoxycholic acid (DCA) in drinking water, both, or left as control for 9 months. For quality control,TQC samples and blanks were also included in the analysis. The two treatments were selected to demonstrate the ability of lipidomics to detect gross changes induced by HFD in the serum and tissue lipidomes, as well as specific/minor changes induced by the secondary bile acid (DCA) through regulation of liver lipid metabolism. The serum and tissue samples were analyzed using targeted and untargeted lipidomics methods. The targeted serum lipidomics data has previously been uploaded as part of study ST001323.
Institute
QIMR Berghofer Medical Research Institute
Last NameMolendijk
First NameJeffrey
Address300 Herston Road, Herston, QLD, 4006, Australia
Emailjeffrey.molendijk@qimrberghofer.edu.au
Phone+61738453992
Submit Date2020-03-26
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2020-04-27
Release Version1
Jeffrey Molendijk Jeffrey Molendijk
https://dx.doi.org/10.21228/M8BX09
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000900
Project DOI:doi: 10.21228/M8BX09
Project Title:Effect of high-fat diet on serum lipidome in mice
Project Summary:We analyzed mouse serum samples from a mouse dietary intervention experiment. Briefly, C57BL/6 mice (n=44) were divided into 4 groups (n=11 per group) and fed High-fat diet (HFD), 1% deoxycholic acid (DCA) in drinking water, both, or left as control for 9 months. For quality control, 12 TQC samples and 2 blanks were also included in the analysis (total 58 samples and 6 groups). The two treatments were selected to demonstrate the ability of lipidomics to detect gross changes induced by HFD in the serum lipidome, as well as specific/minor changes induced by the secondary bile acid (DCA) through regulation of liver lipid metabolism.
Institute:QIMR Berghofer Medical Research Institute
Department:Precision & Systems Biomedicine
Last Name:Mohamed
First Name:Ahmed
Address:300 Herston Road, Herston, QLD, 4006, Australia
Email:ahmed.mohamed@qimrberghofer.edu.au
Phone:+61738453992

Subject:

Subject ID:SU001410
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 Diet BileAcid
SA097335A1_11D1HighFat DCA
SA097336TU_1D1HighFat DCA
SA097337TU_2D1HighFat DCA
SA097338A1_10D1HighFat DCA
SA097339A1_9D1HighFat DCA
SA097340A1_7D1HighFat DCA
SA097341A1_8D1HighFat DCA
SA097342F1_10D1HighFat DCA
SA097343F1_9D1HighFat DCA
SA097344F1_4D1HighFat DCA
SA097345F1_3D1HighFat DCA
SA097346F1_5D1HighFat DCA
SA097347F1_6D1HighFat DCA
SA097348F1_8D1HighFat DCA
SA097349F1_7D1HighFat DCA
SA097350A1_6D1HighFat DCA
SA097351A1_4D1HighFat DCA
SA097352F2_7D1HighFat DCA
SA097353F2_6D1HighFat DCA
SA097354F2_5D1HighFat DCA
SA097355F2_8D1HighFat DCA
SA097356F2_9D1HighFat DCA
SA097357F2_11D1HighFat DCA
SA097358F2_10D1HighFat DCA
SA097359F2_4D1HighFat DCA
SA097360F2_3D1HighFat DCA
SA097361A1_3D1HighFat DCA
SA097362F1_2D1HighFat DCA
SA097363A1_2D1HighFat DCA
SA097364A1_1D1HighFat DCA
SA097365F2_2D1HighFat DCA
SA097366F2_1D1HighFat DCA
SA097367A1_5D1HighFat DCA
SA097368F1_11D1HighFat DCA
SA097369SU_5DHighFat DCA
SA097370SU_7DHighFat DCA
SA097371SU_8DHighFat DCA
SA097372SU_9DHighFat DCA
SA097373SU_4DHighFat DCA
SA097374SU_3DHighFat DCA
SA097375F1_1D1HighFat DCA
SA097376SU_1DHighFat DCA
SA097377SU_2DHighFat DCA
SA097378SU_10DHighFat DCA
SA097379SU_6DHighFat DCA
SA097380TU_6D1HighFat DCA
SA097381TU_5D1HighFat DCA
SA097382TU_11D1HighFat DCA
SA097383TU_3D1HighFat DCA
SA097384TU_7D1HighFat DCA
SA097385TU_4D1HighFat DCA
SA097386TU_8D1HighFat DCA
SA097387TU_10D1HighFat DCA
SA097388SU_11DHighFat DCA
SA097389TU_9D1HighFat DCA
SA097390A1_8C1HighFat water
SA097391A1_11C1HighFat water
SA097392A1_9C1HighFat water
SA097393A1_10C1HighFat water
SA097394A1_5C1HighFat water
SA097395SU_11CHighFat water
SA097396A1_3C1HighFat water
SA097397A1_4C1HighFat water
SA097398A1_6C1HighFat water
SA097399A1_7C1HighFat water
SA097400SU_5CHighFat water
SA097401TU_7C1HighFat water
SA097402TU_6C1HighFat water
SA097403TU_5C1HighFat water
SA097404TU_4C1HighFat water
SA097405TU_8C1HighFat water
SA097406TU_9C1HighFat water
SA097407A1_2C1HighFat water
SA097408TU_11C1HighFat water
SA097409TU_10C1HighFat water
SA097410TU_3C1HighFat water
SA097411TU_2C1HighFat water
SA097412SU_6CHighFat water
SA097413SU_7CHighFat water
SA097414SU_8CHighFat water
SA097415SU_9CHighFat water
SA097416SU_4CHighFat water
SA097417SU_3CHighFat water
SA097418TU_1C1HighFat water
SA097419SU_1CHighFat water
SA097420SU_2CHighFat water
SA097421SU_10CHighFat water
SA097422A1_1C1HighFat water
SA097423F2_4C1HighFat water
SA097424F2_3C1HighFat water
SA097425F2_2C1HighFat water
SA097426F2_5C1HighFat water
SA097427F2_6C1HighFat water
SA097428F2_10C1HighFat water
SA097429F2_9C1HighFat water
SA097430F2_8C1HighFat water
SA097431F2_1C1HighFat water
SA097432F1_3C1HighFat water
SA097433F1_9C1HighFat water
SA097434F1_10C1HighFat water
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Collection:

Collection ID:CO001405
Collection Summary:Mouse serum (30 µL) was added to 215 µL of ice-cold methanol containing 50 µg/mL butylated hydroxytoluene (BHT). Samples were homogenized by three rounds of vortex mixing for 30 seconds, freezing in liquid nitrogen for one minute, thawing for two minutes and sonicating for 10 minutes at 15°C, power 100% in a Grant XUB18 bath sonicator. Tissue wet weight was determined using a Mettler-Toledo XS105 balance (Mettler-Toledo, Melbourne, Australia). Biopsies were transferred to Eppendorf tubes containing 500 µL ice-cold methanol, 50 µg/ml BHT and one steel bead and homogenized in a TissueLyzer LT (Qiagen, Melbourne, Australia) for six minutes at 50 Hz. Homogenate was transferred to new tubes and the original tube was washed with 400 µL methanol and transferred. Samples were dried down under nitrogen flow and resuspended in 20 µL water and 200 µL methanol (50 µg/ml BHT). Samples were homogenized by three rounds of vortex mixing for 30 seconds, freezing in liquid nitrogen for one minute, thawing for two minutes and sonicating for 10 minutes at 15°C, power 100% in a Grant XUB18 bath sonicator. SPLASH LipidoMix Mass Spec Standard (10 µL) and Cer/Sph mixture II (10 µL) internal standards mixes from Avanti Polar Lipids were then added to each sample. After overnight incubation at -30°C, 750 µL MTBE was added and each tube was vortex mixed for 10 seconds and shaken for 10 minutes on a tube rotator (4°C). MilliQ water (188 µL) was then added, and the tube was vortex mixed for 30 seconds to form a biphasic separation. After centrifuging for 15 minutes at 15,000 × g, 700 µL of the clear upper phase containing lipids in MTBE was transferred to another tube and dried down using a gentle stream of nitrogen. After drying down of lipid extracts were resuspended in 50 µL methanol (containing 50 µg/mL BHT)/toluene (90/10%, v/v).
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR001425
Treatment Summary:C57BL/6 mice (n=44) were divided into 4 groups (n=11 per group) and fed High-fat diet (HFD), 1% deoxycholic acid (DCA) in drinking water, both, or left as control for 9 months. The two treatments were selected to demonstrate the ability of lipidomics to detect gross changes induced by HFD in the serum lipidome, as well as specific/minor changes induced by the secondary bile acid (DCA) through regulation of liver lipid metabolism.

Sample Preparation:

Sampleprep ID:SP001418
Sampleprep Summary:Mouse serum (30 µL) was added to 215 µL of ice-cold methanol containing 50 µg/mL butylated hydroxytoluene (BHT). Samples were homogenized by three rounds of vortex mixing for 30 seconds, freezing in liquid nitrogen for one minute, thawing for two minutes and sonicating for 10 minutes at 15°C, power 100% in a Grant XUB18 bath sonicator. Tissue wet weight was determined using a Mettler-Toledo XS105 balance (Mettler-Toledo, Melbourne, Australia). Biopsies were transferred to Eppendorf tubes containing 500 µL ice-cold methanol, 50 µg/ml BHT and one steel bead and homogenized in a TissueLyzer LT (Qiagen, Melbourne, Australia) for six minutes at 50 Hz. Homogenate was transferred to new tubes and the original tube was washed with 400 µL methanol and transferred. Samples were dried down under nitrogen flow and resuspended in 20 µL water and 200 µL methanol (50 µg/ml BHT). Samples were homogenized by three rounds of vortex mixing for 30 seconds, freezing in liquid nitrogen for one minute, thawing for two minutes and sonicating for 10 minutes at 15°C, power 100% in a Grant XUB18 bath sonicator. SPLASH LipidoMix Mass Spec Standard (10 µL) and Cer/Sph mixture II (10 µL) internal standards mixes from Avanti Polar Lipids were then added to each sample. After overnight incubation at -30°C, 750 µL MTBE was added and each tube was vortex mixed for 10 seconds and shaken for 10 minutes on a tube rotator (4°C). MilliQ water (188 µL) was then added, and the tube was vortex mixed for 30 seconds to form a biphasic separation. After centrifuging for 15 minutes at 15,000 × g, 700 µL of the clear upper phase containing lipids in MTBE was transferred to another tube and dried down using a gentle stream of nitrogen. After drying down of lipid extracts were resuspended in 50 µL methanol (containing 50 µg/mL BHT)/toluene (90/10%, v/v).
Processing Storage Conditions:On ice

Combined analysis:

Analysis ID AN002226 AN002227 AN002228 AN002229 AN002230
Analysis type MS MS MS MS MS
Chromatography type HILIC HILIC HILIC Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 1290 Infinity II
Column Agilent HILIC Plus RRHD (100 x 2.1mm,1.8um) Agilent HILIC Plus RRHD (100 x 2.1mm,1.8um) Agilent HILIC Plus RRHD (100 x 2.1mm,1.8um) Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1mm,1.8um) Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1mm,1.8um)
MS Type ESI ESI ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole QTOF QTOF
MS instrument name Agilent 6490 QQQ Agilent 6490 QQQ Agilent 6490 QQQ Agilent 6550 QTOF Agilent 6550 QTOF
Ion Mode UNSPECIFIED POSITIVE UNSPECIFIED POSITIVE POSITIVE
Units Count Count Count Count Count

Chromatography:

Chromatography ID:CH001634
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent HILIC Plus RRHD (100 x 2.1mm,1.8um)
Chromatography Type:HILIC
  
Chromatography ID:CH001635
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent HILIC Plus RRHD (100 x 2.1mm,1.8um)
Chromatography Type:HILIC
  
Chromatography ID:CH001636
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1mm,1.8um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002072
Analysis ID:AN002226
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:-
Ion Mode:UNSPECIFIED
  
MS ID:MS002073
Analysis ID:AN002227
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:-
Ion Mode:POSITIVE
  
MS ID:MS002074
Analysis ID:AN002228
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:-
Ion Mode:UNSPECIFIED
  
MS ID:MS002075
Analysis ID:AN002229
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:-
Ion Mode:POSITIVE
  
MS ID:MS002076
Analysis ID:AN002230
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:-
Ion Mode:POSITIVE
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