Summary of Study ST001837
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 PR001157. The data can be accessed directly via it's Project DOI: 10.21228/M8510S 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 | ST001837 |
Study Title | Quantitative total hexose study on blood serum and ceacal content of rat models |
Study Type | blood serum and caecum content |
Study Summary | Lipids were analyzed in blood serum and cecal content in rat models |
Institute | Helmholtz Centre for Environmental Research |
Department | Department of Molecular Systems biology |
Laboratory | Functional Metabolomics |
Last Name | Rolle-Kampczyk |
First Name | Ulrike |
Address | Permoserstrasse 15, 04318 Leipzig, Germany |
ulrike.rolle-kampczyk@ufz.de | |
Phone | 0049 341 235 1537 |
Submit Date | 2021-06-21 |
Raw Data Available | Yes |
Raw Data File Type(s) | wiff |
Analysis Type Detail | LC-MS |
Release Date | 2021-07-02 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001157 |
Project DOI: | doi: 10.21228/M8510S |
Project Title: | Fecal Transplant from Roux-Y-Gastric-Bypass rat model into a diet induced obesity rat model |
Project Summary: | Investigating alterations in the intestinal microbiome metabolome and host blood metabolome in a diet induced obesity (DIO) rat model after fecal transplant from rats, which underwent Roux-Y-Gastric-Bypass surgery (RYGB). Experimental groups for rat experiments. 1)Rats in the ‘RYGB_Donor group’ underwent RYGB surgery. Postoperatively, animals received a two-choice diet, consisting of a SC and HFD. Once the animals recovered and achieved a stabilized weight reduction at 4 weeks postoperatively, body weight and food intake were recorded daily. 2)Rats allocated into the ‘RYGB_AB group’ were handled the same as animals in the ‘RYGB_donor group’. From postoperative week 4 onwards, animals received an antibiotic treatment (AB) consisting of ampicillin (1 g/l; Ratiopharm), vancomycin (0.5 g/l; Ratiopharm), neomycin (1 g/l; Bela-pharm), and metronidazole (1 g/l; CP-Pharma), provided freshly every day via drinking water.[19, 20] All antibiotics were given for the time period indicated in each figure.[21] 3)Rats in the ‘Lean group’ served as healthy, age-matched controls, constantly kept under SC. 4)Rats in the ‘Lean_AB group’ received the same antibiotic treatment as animals in the RYGB_AB group, serving as a control for antibiotic-specific side effects. All antibiotics were given for the time periods indicated in each figure. 5)Rats in the ‘DIO group’ received no surgery, but were otherwise handled like RYGB litter mates. 6)Rats in the ‘DIO_FMT_RYGB group’ received fecal RYGB_Donor microbiota transplantation once per week, but were otherwise handled like DIO litter mates. For fecal transplantation experiments, 100 mg of fresh stool from body weight-stabilized RYGB donors were re-suspended in 1 ml of PBS, homogenized carefully and administered via oral gavage with 200 μl of the suspension. 7)Rats in the ‘FMT_Lean group’ were handled like DIO litter mates, but were orally gavaged with 200 μl of filtrate received from lean donors, and served as a control for fecal transplantation and specificity of effect size(s) as a function of the donor microbiota. 8)Rats in the ‘DIO_PF_FMT group’ were handled like DIO litter mates, but pair-fed to the SC/HFD food intake of ‘FMT_Lean littermates, serving as a control for effects secondary to reduced caloric intake. |
Institute: | Helmholtz Centre for Environmental Research - UFZ |
Last Name: | Haange |
First Name: | Sven |
Address: | Permoserstrasse 1, Leipzig, Saxony, 04318, Germany |
Email: | sven.haange@ufz.de |
Phone: | 0049 341 2351099 |
Subject:
Subject ID: | SU001914 |
Subject Type: | Mammal |
Subject Species: | Rattus norvegicus |
Taxonomy ID: | 10116 |
Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)
mb_sample_id | local_sample_id | Tissue | Sample treatment |
---|---|---|---|
SA170829 | 1024038893 | Caecum | DIO |
SA170830 | 1024038923 | Caecum | DIO |
SA170831 | 1024041378 | Caecum | DIO |
SA170832 | 1024038919 | Caecum | DIO |
SA170833 | 1024041363 | Caecum | DIO |
SA170834 | 1024038904 | Caecum | DIO |
SA170835 | 1024038651 | Caecum | DIO |
SA170836 | 1024041295 | Caecum | DIO |
SA170837 | 1024041276 | Caecum | DIO |
SA170838 | 1024041219 | Caecum | DIO |
SA170839 | 1024041238 | Caecum | DIO_AB |
SA170840 | 1024041261 | Caecum | DIO_AB |
SA170841 | 1024035756 | Caecum | DIO_AB |
SA170842 | 1024041223 | Caecum | DIO_AB |
SA170843 | 1024041242 | Caecum | DIO_AB |
SA170844 | 1024035775 | Caecum | DIO_AB |
SA170845 | 1024038889 | Caecum | DIO_FMT_RYGB |
SA170846 | 1024038841 | Caecum | DIO_FMT_RYGB |
SA170847 | 1024038874 | Caecum | DIO_FMT_RYGB |
SA170848 | 1024038860 | Caecum | DIO_FMT_RYGB |
SA170849 | 1024041257 | Caecum | DIO_FMT_RYGB |
SA170850 | 1024041382 | Caecum | DIO_FMT_RYGB |
SA170851 | 1024038666 | Caecum | DIO_FMT_RYGB |
SA170852 | 1024038671 | Caecum | DIO_FMT_RYGB |
SA170853 | 1024041325 | Caecum | DIO_FMT_RYGB |
SA170854 | 1024041281 | Caecum | DIO_FMT_RYGB |
SA170855 | 1024038981 | Caecum | DIO_PF_FMT |
SA170856 | 1024038938 | Caecum | DIO_PF_FMT |
SA170857 | 1024038942 | Caecum | DIO_PF_FMT |
SA170858 | 1024038961 | Caecum | DIO_PF_FMT |
SA170859 | 1024038957 | Caecum | DIO_PF_FMT |
SA170860 | 1024038976 | Caecum | DIO_PF_FMT |
SA170861 | 1024041408 | Caecum | FMT_lean |
SA170862 | 1024041397 | Caecum | FMT_lean |
SA170863 | 1024041359 | Caecum | FMT_lean |
SA170864 | 1024041330 | Caecum | FMT_lean |
SA170865 | 1024041344 | Caecum | FMT_lean |
SA170866 | 1024035761 | Caecum | FMT_lean |
SA170867 | 1024038768 | Caecum | Lean |
SA170868 | 1024041306 | Caecum | Lean |
SA170869 | 1024041311 | Caecum | Lean |
SA170870 | 1024038753 | Caecum | Lean |
SA170871 | 1024039026 | Caecum | Lean |
SA170872 | 1024039011 | Caecum | Lean |
SA170873 | 1024038791 | Caecum | Lean |
SA170874 | 1024038995 | Caecum | Lean |
SA170875 | 1024038802 | Caecum | Lean |
SA170876 | 1024039007 | Caecum | Lean |
SA170877 | 1024032797 | Caecum | Lean_AB |
SA170878 | 1024032782 | Caecum | Lean_AB |
SA170879 | 1024038787 | Caecum | Lean_AB |
SA170880 | 1024038749 | Caecum | Lean_AB |
SA170881 | 1024038772 | Caecum | Lean_AB |
SA170882 | 1024038734 | Caecum | Lean_AB |
SA170883 | 1024032759 | Caecum | RYGB_AB |
SA170884 | 1024038720 | Caecum | RYGB_AB |
SA170885 | 1024038685 | Caecum | RYGB_AB |
SA170886 | 1024032763 | Caecum | RYGB_AB |
SA170887 | 1024032778 | Caecum | RYGB_AB |
SA170888 | 1024038690 | Caecum | RYGB_AB |
SA170889 | 1024041465 | Caecum | RYGB_AB |
SA170890 | 1024041484 | Caecum | RYGB_AB |
SA170891 | 1024041446 | Caecum | RYGB_AB |
SA170892 | 1024032744 | Caecum | RYGB_Donor |
SA170893 | 1024041427 | Caecum | RYGB_Donor |
SA170894 | 1024041412 | Caecum | RYGB_Donor |
SA170895 | 1024041451 | Caecum | RYGB_Donor |
SA170896 | 1024038836 | Caecum | RYGB_Donor |
SA170897 | 1024038701 | Caecum | RYGB_Donor |
SA170898 | 1024038715 | Caecum | RYGB_Donor |
SA170899 | 1024041431 | Caecum | RYGB_Donor |
SA170900 | 1024038821 | Caecum | RYGB_Donor |
SA170901 | 1024033074 | Plasma | DIO |
SA170902 | 1024033093 | Plasma | DIO |
SA170903 | 1024033060 | Plasma | DIO |
SA170904 | 1024033089 | Plasma | DIO |
SA170905 | 1024033041 | Plasma | DIO_FMT_RYGB |
SA170906 | 1024033055 | Plasma | DIO_FMT_RYGB |
SA170907 | 1024033021 | Plasma | DIO_FMT_RYGB |
SA170908 | 1024033036 | Plasma | DIO_FMT_RYGB |
SA170909 | 1024035794 | Plasma | DIO_PF_FMT |
SA170910 | 1024033104 | Plasma | DIO_PF_FMT |
SA170911 | 1024033119 | Plasma | DIO_PF_FMT |
SA170912 | 1024035805 | Plasma | DIO_PF_FMT |
SA170913 | 1024035810 | Plasma | DIO_PF_FMT |
SA170914 | 1024035780 | Plasma | DIO_PF_FMT |
SA170915 | 1024035858 | Plasma | Lean |
SA170916 | 1024035839 | Plasma | Lean |
SA170917 | 1024035843 | Plasma | Lean |
SA170918 | 1024035824 | Plasma | Lean |
SA170919 | 1024033017 | Plasma | RYGB_AB |
SA170920 | 1024032991 | Plasma | RYGB_AB |
SA170921 | 1024032971 | Plasma | RYGB_AB |
SA170922 | 1024032986 | Plasma | RYGB_Donor |
SA170923 | 1024032948 | Plasma | RYGB_Donor |
SA170924 | 1024032933 | Plasma | RYGB_Donor |
SA170925 | 1024032952 | Plasma | RYGB_Donor |
SA170926 | 1024041174 | Serum | DIO |
SA170927 | 1024041155 | Serum | DIO |
SA170928 | 1024032623 | Serum | DIO |
Collection:
Collection ID: | CO001907 |
Collection Summary: | Animals were sacrificed, blood and cecum tissue were removed, snap frozen in liquid nitrogen and stored at -80°C until further analysis |
Sample Type: | Cecum |
Treatment:
Treatment ID: | TR001927 |
Treatment Summary: | RYGB surgery was performed on age-matched (8-10-weeks old) male Wistar IGS rats. After four weeks of recovery, animals were put on an antibiotic cocktail consisting of ampicillin (1 g/l; Ratiopharm), vancomycin (0.5 g/l; Ratiopharm), neomycin (1 g/l; Bela-pharm), and metronidazole (1 g/l; CP-Pharma), provided freshly every day via drinking water. The parallel FMT group received fecal RYGB microbiota transplantation once per week, but were otherwise handled like DIO littermates. For fecal transplantation experiments, 100 mg of fresh stool from bodyweight-stabilized RYGB donors was re-suspended in 1 ml of PBS, homogenized carefully and administered via oral gavage with 200 μl of the suspension. |
Sample Preparation:
Sampleprep ID: | SP001920 |
Sampleprep Summary: | Sample preparation for MetIDQ p180 Kit measurement Solvents: Acetonitril (Merck KGaA, Darmstadt, Germany hypergrade for LC-MS) Water MiliQ, Extracting agent - ACN / H2O (1:1) Equipment 4 steel balls size M Eppendorf Tubes 2mL Tissue slicer (Rettberg, Germany) Centrifuge (Sigma) Work steps Approximately 100mg of caecum sample and 4 steel balls of size M into each tube. Per mg of sample 5µL of extracting agent was added. Shake the samples for 10 minutes at 30 Hz in the tissue slicer and centrifuge for 2 minutes at 14000 rpm. 10 µL supernatant was used for the targeted analytics. Blood serum samples 10 µL were used for analysis Kit reparation The analysis was performed using the validated MetIDQ p180 Kit and described in Siskos et al. [1]. Data processing was carried out with the provided quantitation method Kit (Biocrates Life Sciences AG, Innsbruck, Austria). 1 Siskos AP, Jain P, Römisch-Margl W, Bennett M, Achaintre D, Asad Y, et al. Interlaboratory Reproducibility of a Targeted Metabolomics Platform for Analysis of Human Serum and Plasma. Anal Chem 2017;89:656-65. |
Combined analysis:
Analysis ID | AN002979 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | UPLC (Waters Acquity, Waters Corporation, Milford, USA) |
Column | Agilent Zorbax Eclipse XDB C18 (100 x 3.0mm,3.5um) |
MS Type | ESI |
MS instrument type | Triple quadrupole |
MS instrument name | ABI Sciex 5500 QTrap |
Ion Mode | NEGATIVE |
Units | µM |
Chromatography:
Chromatography ID: | CH002208 |
Chromatography Summary: | LC - Instrument Parameters AbsoluteIDQ® p180 Kit (Biocrates Life Science AG, Innsbruck, Austria) System: UPLC (Waters Acquity, Waters Corporation, Milford, USA) Column: Agilent, Zorbax Eclipse XDB C18, 3.0 x 100 mm, 3.5 μM, Agilent Waldbronn, Germany Precolumn: Security Guard, Phenomenex, C18, 4 x 3 mm; Phenomenex, Aschaffenburg, Germany Materials: Water MiliQ, Methanol (Merck KGaA, Darmstadt, Germany, hypergrade for LC-MS) Acetonitril (Merck KGaA, Darmstadt, Germany hypergrade for LC-MS) Ammonium Acetate (Honeywell - Fluka, Seelze, Germany) Formic Acid (Honeywell, Fluka, Seelze, Germany) Running Solvent: 5mM ammonium acetat in methanol LC: A: 2mL Formic acid in MilliQ water B: 1mL Formic Acid in Acetonitrile Gradient Table LC Time (min) Flow Rate (mL/min) %A %B Curve Initial 0.500 100.0 0.0 Initial 0.50 0.500 100.0 0.0 6 4.00 0.500 30.0 70.0 6 5.30 0.500 30.0 70.0 6 5.40 0.500 100.0 0.0 6 7.30 0.500 100.0 0.0 6 |
Methods Filename: | LC_parameters.pdf |
Instrument Name: | UPLC (Waters Acquity, Waters Corporation, Milford, USA) |
Column Name: | Agilent Zorbax Eclipse XDB C18 (100 x 3.0mm,3.5um) |
Flow Gradient: | FIA Time (min) Flow Rate (mL/min) %A %B Curve Initial 0.030 0.0 100.0 Initial 1.60 0.030 0.0 100.0 6 2.40 0.200 0.0 100.0 6 2.80 0.200 0.0 100.0 6 3.00 0.030 0.0 100.0 6 |
Flow Rate: | 0.03ml/min |
Solvent A: | 100% methanol; 5mM ammonium acetate |
Solvent B: | 50% methanol/50% water; 5mM ammonium acetate |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS002769 |
Analysis ID: | AN002979 |
Instrument Name: | ABI Sciex 5500 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | Analyst version 1.6 Software from SCIEX. For Validation METIDQ Software version Boron from Biocrates |
Ion Mode: | NEGATIVE |
Analysis Protocol File: | MS_parameters_1.pdf |