Summary of Study ST003458

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 PR002122. The data can be accessed directly via it's Project DOI: 10.21228/M8B52G 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	ST003458
Study Title	Metabolomics of mice kidney to support understanding of early metabolic shift in presymptomatic sepsis patients. (Part4 mice kidney metabolite)
Study Summary	Sepsis, a life-threatening organ dysfunction caused by a dysregulated response to infection, is a critical medical condition with significant global impact, responsible for 48.9 million cases and 11 million deaths annually. Metabolic dysregulation in sepsis is a critical determinant of disease outcome, yet most studies focus on patients after severe illness onset, comparing septic versus non-septic groups or survivors versus non-survivors. To truly understand this complex disease, it is essential to investigate early metabolic shifts, capturing the transition from simple infection to sepsis. Our untargeted metabolome analysis of kidney tissues from mice model revealed early septic biomarkers in kidney.
Institute	Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute
Department	Microbiome Dynamics
Last Name	XU
First Name	LINLIN
Address	Beutenbergstraße 11a, Jena, Thuringia, 07745, Germany
Email	Lin-Lin.Xu@hki-jena.de
Phone	+4936415321265
Submit Date	2024-09-04
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-05-26
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002122
Project DOI:	doi: 10.21228/M8B52G
Project Title:	Early Metabolic Shifts in the Sepsis: Insights from Presymptomatic Patients and In Vivo Models.
Project Type:	MS quantitative analysis
Project Summary:	Metabolomics of human serum to support understanding of early metabolic shift in presymptomatic sepsis patients and further confirmed in in vivo model.
Institute:	Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute
Department:	Microbiome Dynamics
Last Name:	XU
First Name:	LINLIN
Address:	Beutenbergstraße 11a, Jena, Thuringia, 07745, Germany
Email:	Lin-Lin.Xu@leibniz-hki.de
Phone:	+4936415321265

Subject:

Subject ID:	SU003586
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammals

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Group
SA382693	Blank_003	blank	Blank
SA382694	Blank_002	blank	Blank
SA382695	Blank_001	blank	Blank
SA382696	Blank_PB	blank	Blank
SA382697	Blank_004	blank	Blank
SA382664	SA021018	Kidney	CLP (24h) / 12C-Serin
SA382665	SA020976	Kidney	CLP (24h) / 12C-Serin
SA382666	SA021025	Kidney	CLP (24h) / 12C-Serin
SA382667	SA020983	Kidney	CLP (24h) / 12C-Serin
SA382668	SA020941	Kidney	CLP (24h) / 13C-Serin
SA382669	SA020934	Kidney	CLP (24h) / 13C-Serin
SA382670	SA020888	Kidney	CLP (24h) / 13C-Serin
SA382671	SA020881	Kidney	CLP (24h) / 13C-Serin
SA382672	SA020969	Kidney	CLP (24h) / Vehicle
SA382673	SA020923	Kidney	CLP (24h) / Vehicle
SA382674	SA020895	Kidney	CLP (24h) / Vehicle
SA382675	QC_007	Kidney	QC
SA382676	QC_006	Kidney	QC
SA382677	QC_008	Kidney	QC
SA382678	QC_005	Kidney	QC
SA382679	QC_001	Kidney	QC
SA382680	QC_004	Kidney	QC
SA382681	QC_009	Kidney	QC
SA382682	SA020997	Kidney	Sham / 12C-Serin
SA382683	SA020990	Kidney	Sham / 12C-Serin
SA382684	SA021004	Kidney	Sham / 12C-Serin
SA382685	SA021011	Kidney	Sham / 12C-Serin
SA382686	SA020962	Kidney	Sham / 13C-Serin
SA382687	SA020909	Kidney	Sham / 13C-Serin
SA382688	SA020902	Kidney	Sham / 13C-Serin
SA382689	SA020955	Kidney	Sham / 13C-Serin
SA382690	SA020928	Kidney	Sham / Vehicle
SA382691	SA020916	Kidney	Sham / Vehicle
SA382692	SA020948	Kidney	Sham / Vehicle

Showing results 1 to 34 of 34

Showing results 1 to 34 of 34

Collection:

Collection ID:	CO003579
Collection Summary:	Mice tissue samples were collected from our in vivo mice model and frozen at -80 °C. Samples were shipped to MS-OMICS for metabolomic analysis.
Sample Type:	Kidney

Treatment:

Treatment ID:	TR003595
Treatment Summary:	Approximately 30% of the cecum was ligated and punctured twice with a 23 Gauge (G) needle. A small amount of faeces was extruded and the cecum was placed back into the abdominal cavity. All animals received 40 mL/kg saline s.c. directly after the procedure and once 25mg/kg s.c. Imipenem/Cilastatin after 6 hours. This model is associated with a 14-day mortality of 30%, closely mimicking the clinical situation. Animals were orally gavaged with 500mg/kg 12C-Serin (Sigma) or 13C-Serin (CLM-1574-H-0.25 Serine-L (13C3 99%13C), Euroisotope, Germany) in 10mL/kg drinking water or drinking water only (vehicle) 6 and 18 hours after CLP98,99. After 24 hours, the animals are then perfused with ice cold PBS and organs were harvested, snap frozen and stored at -80° until further analysis. Sham animals underwent exactly to the same procedures except for the CLP.

Treatment ID:

TR003595

Treatment Summary:

Approximately 30% of the cecum was ligated and punctured twice with a 23 Gauge (G) needle. A small amount of faeces was extruded and the cecum was placed back into the abdominal cavity. All animals received 40 mL/kg saline s.c. directly after the procedure and once 25mg/kg s.c. Imipenem/Cilastatin after 6 hours. This model is associated with a 14-day mortality of 30%, closely mimicking the clinical situation. Animals were orally gavaged with 500mg/kg 12C-Serin (Sigma) or 13C-Serin (CLM-1574-H-0.25 Serine-L (13C3 99%13C), Euroisotope, Germany) in 10mL/kg drinking water or drinking water only (vehicle) 6 and 18 hours after CLP98,99. After 24 hours, the animals are then perfused with ice cold PBS and organs were harvested, snap frozen and stored at -80° until further analysis. Sham animals underwent exactly to the same procedures except for the CLP.

Sample Preparation:

Sampleprep ID:	SP003593
Sampleprep Summary:	To prepare samples for semi-polar metabolites extraction, the different tissue samples were weighted and transferred to Eppendorf tubes. Ceramic beads and precooled methanol/water (1:2) were added. All tubes were placed in a pre-cooled (-20°C) bead beater and homogenized (4 x 30 sec., 30 Hz) followed by ultrasonication (5 min). After centrifugation (18000 RCF, 5 min, 4°C), the supernatant was collected. The sample pellet was reextracted as described above. The two extract supernatants were pooled and passed through a phosphor removal cartridge (Phree filter plates). A precise aliquot of the extract was evaporated to dryness under a gentle stream of nitrogen, before reconstitution with 10% Eluent B in Eluent A. All Samples were diluted 5 times in mobile phase eluent A and stable isotope labelled standards were added before analysis. Mouse serum (50 μl) was diluted with a mixture of acetonitrile and methanol (200 μl 1:1 v/v). The extract was then passed through a phosphor removal cartridge (Phree, Phenomenex). An aliquot (100 μl) was transferred into a high recovery HPLC vial and the solvent was removed under a gentle flow of nitrogen. Extracts were reconstituted in a mobile phase mixture (100 μl, 10%B in 90%A). To ensure high-quality sample preparation, a quality control sample (QC sample) was prepared by pooling small equal aliquots from each sample, to create a representative average of the entire set.

Sampleprep ID:

SP003593

Sampleprep Summary:

To prepare samples for semi-polar metabolites extraction, the different tissue samples were weighted and transferred to Eppendorf tubes. Ceramic beads and precooled methanol/water (1:2) were added. All tubes were placed in a pre-cooled (-20°C) bead beater and homogenized (4 x 30 sec., 30 Hz) followed by ultrasonication (5 min). After centrifugation (18000 RCF, 5 min, 4°C), the supernatant was collected. The sample pellet was reextracted as described above. The two extract supernatants were pooled and passed through a phosphor removal cartridge (Phree filter plates). A precise aliquot of the extract was evaporated to dryness under a gentle stream of nitrogen, before reconstitution with 10% Eluent B in Eluent A. All Samples were diluted 5 times in mobile phase eluent A and stable isotope labelled standards were added before analysis. Mouse serum (50 μl) was diluted with a mixture of acetonitrile and methanol (200 μl 1:1 v/v). The extract was then passed through a phosphor removal cartridge (Phree, Phenomenex). An aliquot (100 μl) was transferred into a high recovery HPLC vial and the solvent was removed under a gentle flow of nitrogen. Extracts were reconstituted in a mobile phase mixture (100 μl, 10%B in 90%A). To ensure high-quality sample preparation, a quality control sample (QC sample) was prepared by pooling small equal aliquots from each sample, to create a representative average of the entire set.

Chromatography:

Chromatography ID:	CH004314
Instrument Name:	Thermo Vanquish
Column Name:	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:	30
Flow Gradient:	0-2 min: 0 % B, 4 min 35% B, 6-14 min 90% B, 14.1-15 min 0% B.
Flow Rate:	0.3mL/min
Solvent A:	100% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:	100% methanol; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:	Reversed phase

Analysis:

Analysis ID:	AN005681
Laboratory Name:	MS-Omics, Denmark
Analysis Type:	MS
Analysis Protocol File:	Doneanu_etal.pdf
Chromatography ID:	CH004314
Num Factors:	8
Num Metabolites:	134
Has Rt:	1
Rt Units:	Minutes
Results File:	ST003458_AN005681_Results.txt
Units:	Normalized peak area

Analysis ID:	AN005682
Laboratory Name:	MS-Omics, Denmark
Analysis Type:	MS
Analysis Protocol File:	Doneanu_etal.pdf
Chromatography ID:	CH004314
Num Factors:	8
Num Metabolites:	71
Has Rt:	1
Rt Units:	Minutes
Results File:	ST003458_AN005682_Results.txt
Units:	Normalized peak area