Summary of Study ST001832

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.

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Study IDST001832
Study TitleQuantitative bile acids study on blood serum and ceacal content of rat models (part I)
Study Typeblood serum and caecum content
Study SummaryBile acids were analyzed in blood serum and cecal content in rat models
Institute
Helmholtz Centre for Environmental Research
DepartmentDepartment of Molecular Systems biology
LaboratoryFunctional Metabolomics
Last NameRolle-Kampczyk
First NameUlrike
AddressPermoserstrasse 15, 04318 Leipzig, Germany
Emailulrike.rolle-kampczyk@ufz.de
Phone0049 341 235 1537
Submit Date2021-06-15
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2021-07-02
Release Version1
Ulrike Rolle-Kampczyk Ulrike Rolle-Kampczyk
https://dx.doi.org/10.21228/M8510S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU001909
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id Tissue
SA1703411024041020Caecum | Sample treatment:DIO
SA1703501024041673Caecum | Sample treatment:DIO
SA1703511024039031Caecum | Sample treatment:DIO
SA1703521024039045Caecum | Sample treatment:DIO
SA1703531024039050Caecum | Sample treatment:DIO
SA1703661024040931Caecum | Sample treatment:DIO
SA1703961024041499Caecum | Sample treatment:DIO
SA1704011024040999Caecum | Sample treatment:DIO
SA1704041024041015Caecum | Sample treatment:DIO
SA1703721024040946Caecum | Sample treatment:DIO_AB
SA1703821024040951Caecum | Sample treatment:DIO_AB
SA1703871024038632Caecum | Sample treatment:DIO_AB
SA1703891024035907Caecum | Sample treatment:DIO_AB
SA1703901024040965Caecum | Sample treatment:DIO_AB
SA1703971024040984Caecum | Sample treatment:DIO_AB
SA1703461024041034Caecum | Sample treatment:DIO_FMT_RYGB
SA1703471024041635Caecum | Sample treatment:DIO_FMT_RYGB
SA1703481024041640Caecum | Sample treatment:DIO_FMT_RYGB
SA1703541024041049Caecum | Sample treatment:DIO_FMT_RYGB
SA1703551024041654Caecum | Sample treatment:DIO_FMT_RYGB
SA1703561024041669Caecum | Sample treatment:DIO_FMT_RYGB
SA1703921024035931Caecum | Sample treatment:DIO_FMT_RYGB
SA1703941024040970Caecum | Sample treatment:DIO_FMT_RYGB
SA1703981024041514Caecum | Sample treatment:DIO_FMT_RYGB
SA1704021024041001Caecum | Sample treatment:DIO_FMT_RYGB
SA1703491024039079Caecum | Sample treatment:DIO_PF_FMT
SA1703571024039083Caecum | Sample treatment:DIO_PF_FMT
SA1703581024039098Caecum | Sample treatment:DIO_PF_FMT
SA1703591024039109Caecum | Sample treatment:DIO_PF_FMT
SA1703601024039113Caecum | Sample treatment:DIO_PF_FMT
SA1703881024035896Caecum | Sample treatment:FMT_lean
SA1703931024035945Caecum | Sample treatment:FMT_lean
SA1703951024035964Caecum | Sample treatment:FMT_lean
SA1703991024041529Caecum | Sample treatment:FMT_lean
SA1704001024041533Caecum | Sample treatment:FMT_lean
SA1703371024039132Caecum | Sample treatment:Lean
SA1703611024039147Caecum | Sample treatment:Lean
SA1703621024039151Caecum | Sample treatment:Lean
SA1703711024038481Caecum | Sample treatment:Lean
SA1703731024038496Caecum | Sample treatment:Lean
SA1703761024038526Caecum | Sample treatment:Lean
SA1703771024038531Caecum | Sample treatment:Lean
SA1703911024035926Caecum | Sample treatment:Lean
SA1704031024039128Caecum | Sample treatment:Lean
SA1703691024038462Caecum | Sample treatment:Lean_AB
SA1703701024038477Caecum | Sample treatment:Lean_AB
SA1703741024038507Caecum | Sample treatment:Lean_AB
SA1703751024038511Caecum | Sample treatment:Lean_AB
SA1703851024038613Caecum | Sample treatment:Lean_AB
SA1703861024038628Caecum | Sample treatment:Lean_AB
SA1703421024041586Caecum | Sample treatment:RYGB_AB
SA1703441024041591Caecum | Sample treatment:RYGB_AB
SA1703451024041621Caecum | Sample treatment:RYGB_AB
SA1703631024041053Caecum | Sample treatment:RYGB_AB
SA1703641024041072Caecum | Sample treatment:RYGB_AB
SA1703681024041102Caecum | Sample treatment:RYGB_AB
SA1703811024038579Caecum | Sample treatment:RYGB_AB
SA1703831024038583Caecum | Sample treatment:RYGB_AB
SA1703841024038609Caecum | Sample treatment:RYGB_AB
SA1703381024041548Caecum | Sample treatment:RYGB_Donor
SA1703391024041552Caecum | Sample treatment:RYGB_Donor
SA1703401024041567Caecum | Sample treatment:RYGB_Donor
SA1703431024041571Caecum | Sample treatment:RYGB_Donor
SA1703651024041087Caecum | Sample treatment:RYGB_Donor
SA1703671024041091Caecum | Sample treatment:RYGB_Donor
SA1703781024038545Caecum | Sample treatment:RYGB_Donor
SA1703791024038550Caecum | Sample treatment:RYGB_Donor
SA1703801024038564Caecum | Sample treatment:RYGB_Donor
SA1704091024038458Serum | Sample treatment:DIO
SA1704181024033195Serum | Sample treatment:DIO
SA1704191024033206Serum | Sample treatment:DIO
SA1704201024033211Serum | Sample treatment:DIO
SA1704211024033225Serum | Sample treatment:DIO
SA1704311024038375Serum | Sample treatment:DIO
SA1704621024035363Serum | Sample treatment:DIO
SA1704641024035378Serum | Sample treatment:DIO
SA1704701024038443Serum | Sample treatment:DIO
SA1704361024038380Serum | Sample treatment:DIO_AB
SA1704461024038394Serum | Sample treatment:DIO_AB
SA1704511024035261Serum | Sample treatment:DIO_AB
SA1704531024035281Serum | Sample treatment:DIO_AB
SA1704541024038405Serum | Sample treatment:DIO_AB
SA1704631024038424Serum | Sample treatment:DIO_AB
SA1704131024032366Serum | Sample treatment:DIO_FMT_RYGB
SA1704141024033157Serum | Sample treatment:DIO_FMT_RYGB
SA1704151024033161Serum | Sample treatment:DIO_FMT_RYGB
SA1704221024032371Serum | Sample treatment:DIO_FMT_RYGB
SA1704571024035311Serum | Sample treatment:DIO_FMT_RYGB
SA1704591024038410Serum | Sample treatment:DIO_FMT_RYGB
SA1704651024035382Serum | Sample treatment:DIO_FMT_RYGB
SA1704681024038439Serum | Sample treatment:DIO_FMT_RYGB
SA1704161024033230Serum | Sample treatment:DIO_PF_FMT
SA1704171024033244Serum | Sample treatment:DIO_PF_FMT
SA1704231024033259Serum | Sample treatment:DIO_PF_FMT
SA1704241024033282Serum | Sample treatment:DIO_PF_FMT
SA1704521024035276Serum | Sample treatment:FMT_lean
SA1704581024035325Serum | Sample treatment:FMT_lean
SA1704601024035330Serum | Sample treatment:FMT_lean
SA1704611024035359Serum | Sample treatment:FMT_lean
SA1704661024035397Serum | Sample treatment:FMT_lean
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 134

Collection:

Collection ID:CO001902
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:TR001922
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 body weight-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:SP001915
Sampleprep Summary: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 To approximately 100 mg of sample four steel balls of size M rae added in Eppendorf tubes. Then add for each mg of sample 5 µL of extracting agent. Shake the samples for 10 minutes at 30 Hz in the tissue slicer and centrifuge for 2 minutes at 14000 rpm. The supernatant is used for targeted analytics as described in the kit manufactures manual. Kit measurement The analysis was performed using the validated Bile Acid Kit (Biocrates Life Sciences, Inssbruck, Austria) as described in Pham et al. 2017 [1]. Data processing is carried out with the provided quantitation method Kit (Biocrates Life Sciences AG, Innsbruck, Austria). 1 Pham HT, Arnhard K, Asad YJ, Deng L, Felder TK, St John-Williams L, et al. Inter-Laboratory Robustness of Next-Generation Bile Acid Study in Mice and Humans: International Ring Trial Involving 12 Laboratories. The Journal of Applied Laboratory Medicine 2019;1:129-42.

Combined analysis:

Analysis ID AN002974
Analysis type MS
Chromatography type Reversed phase
Chromatography system UPLC (Waters Acquity, Waters Corporation, Milford, USA)
Column none
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode NEGATIVE
Units µM

Chromatography:

Chromatography ID:CH002203
Instrument Name:UPLC (Waters Acquity, Waters Corporation, Milford, USA)
Column Name:none
Chromatography Type:Reversed phase

MS:

MS ID:MS002764
Analysis ID:AN002974
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
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