Summary of Study ST003465

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	ST003465
Study Title	Lipidomics of mice kidney to support understanding of early metabolic shift in presymptomatic sepsis patients. (Part10 mice kidney lipid)
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 lipidome analysis of kidney 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	2024-09-05
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:	SU003593
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Gender:	Not applicable
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
SA382945	Blank_003	blank	Blank
SA382946	Blank_002	blank	Blank
SA382947	Blank_001	blank	Blank
SA382948	Blank_PB	blank	Blank
SA382949	Blank_004	blank	Blank
SA382916	SA021018	Kidney	CLP (24h) / 12C-Serin
SA382917	SA020976	Kidney	CLP (24h) / 12C-Serin
SA382918	SA021025	Kidney	CLP (24h) / 12C-Serin
SA382919	SA020983	Kidney	CLP (24h) / 12C-Serin
SA382920	SA020941	Kidney	CLP (24h) / 13C-Serin
SA382921	SA020934	Kidney	CLP (24h) / 13C-Serin
SA382922	SA020888	Kidney	CLP (24h) / 13C-Serin
SA382923	SA020881	Kidney	CLP (24h) / 13C-Serin
SA382924	SA020969	Kidney	CLP (24h) / Vehicle
SA382925	SA020923	Kidney	CLP (24h) / Vehicle
SA382926	SA020895	Kidney	CLP (24h) / Vehicle
SA382927	QC_007	Kidney	QC
SA382928	QC_006	Kidney	QC
SA382929	QC_008	Kidney	QC
SA382930	QC_005	Kidney	QC
SA382931	QC_001	Kidney	QC
SA382932	QC_004	Kidney	QC
SA382933	QC_009	Kidney	QC
SA382934	SA020997	Kidney	Sham / 12C-Serin
SA382935	SA020990	Kidney	Sham / 12C-Serin
SA382936	SA021004	Kidney	Sham / 12C-Serin
SA382937	SA021011	Kidney	Sham / 12C-Serin
SA382938	SA020962	Kidney	Sham / 13C-Serin
SA382939	SA020909	Kidney	Sham / 13C-Serin
SA382940	SA020902	Kidney	Sham / 13C-Serin
SA382941	SA020955	Kidney	Sham / 13C-Serin
SA382942	SA020928	Kidney	Sham / Vehicle
SA382943	SA020916	Kidney	Sham / Vehicle
SA382944	SA020948	Kidney	Sham / Vehicle

Showing results 1 to 34 of 34

Showing results 1 to 34 of 34

Collection:

Collection ID:	CO003586
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:	TR003602
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:

TR003602

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:	SP003600
Sampleprep Summary:	In the different tissue samples, the pellet from the semipolar extraction were used to extract lipids as follows. DCM:MeOH (3:1) were added to the pellets, and the samples were homogenized using a pre-cooled Bead-beater (4 x 60 sec at 30 Hz), with colling of the blocks between the beading cycles. Subsequently, the samples were ultrasonicate for 5 mins and centrifuged (5 mins, 1800 RCF, 4 °C). The supernatant were collected and dried under nitrogen gas. Samples were then reconstitute with 6x (spleen and WAT) or 3x (heart, liver and kidney) the sample weight with the reconstitution solvent eluent mix and vortex mixed for 30 sec. The reconstituted samples were filtrated using SpinX filters by centrifugation (5 mins, 1800 RCF, 4 °C). All samples were mixed 1: 50 in eluent mix. For serum samples, an alliqoute of the serum samples are mixed with extraction solvent (0.1 M BHT in isopropanol with stable isotope labelled internal standard) in a Spin-X® filter. The filters were vortex-mixed for 60 sec and left at room temperature for 10 mins before placing in -20 °C Freezer overnight. The following day samples were left at room temperature for 30 mins before centrifuging (1800g /4°C/2 min). The filtrate were mixed with eluent mix 1:3.

Sampleprep ID:

SP003600

Sampleprep Summary:

In the different tissue samples, the pellet from the semipolar extraction were used to extract lipids as follows. DCM:MeOH (3:1) were added to the pellets, and the samples were homogenized using a pre-cooled Bead-beater (4 x 60 sec at 30 Hz), with colling of the blocks between the beading cycles. Subsequently, the samples were ultrasonicate for 5 mins and centrifuged (5 mins, 1800 RCF, 4 °C). The supernatant were collected and dried under nitrogen gas. Samples were then reconstitute with 6x (spleen and WAT) or 3x (heart, liver and kidney) the sample weight with the reconstitution solvent eluent mix and vortex mixed for 30 sec. The reconstituted samples were filtrated using SpinX filters by centrifugation (5 mins, 1800 RCF, 4 °C). All samples were mixed 1: 50 in eluent mix. For serum samples, an alliqoute of the serum samples are mixed with extraction solvent (0.1 M BHT in isopropanol with stable isotope labelled internal standard) in a Spin-X® filter. The filters were vortex-mixed for 60 sec and left at room temperature for 10 mins before placing in -20 °C Freezer overnight. The following day samples were left at room temperature for 30 mins before centrifuging (1800g /4°C/2 min). The filtrate were mixed with eluent mix 1:3.

Chromatography:

Chromatography ID:	CH004322
Methods Filename:	Doneanu_etal.pdf
Instrument Name:	Thermo Vanquish
Column Name:	Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:	55
Flow Gradient:	0-2 min: 40 % B, 2.1 min 50% B, 12 min 54% B, 12.1 min 70% B, 18-20 min 99 % B, 20.1-22 min 40% B
Flow Rate:	0.4mL/min
Solvent A:	60% Acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:	90% Isopropanol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:	Reversed phase

Analysis:

Analysis ID:	AN005695
Laboratory Name:	MS-Omics, Denmark
Analysis Type:	MS
Analysis Protocol File:	Doneanu_etal.pdf
Chromatography ID:	CH004322
Num Factors:	8
Num Metabolites:	252
Has Rt:	1
Rt Units:	Minutes
Results File:	ST003465_AN005695_Results.txt
Units:	Normalized peak area

Analysis ID:	AN005696
Laboratory Name:	MS-Omics, Denmark
Analysis Type:	MS
Analysis Protocol File:	Doneanu_etal.pdf
Chromatography ID:	CH004322
Num Factors:	8
Num Metabolites:	76
Has Rt:	1
Rt Units:	Minutes
Results File:	ST003465_AN005696_Results.txt
Units:	Normalized peak area