Summary of Study ST001294

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 PR000876. The data can be accessed directly via it's Project DOI: 10.21228/M8FX1M This work is supported by NIH grant, U2C- DK119886.

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Study IDST001294
Study TitleEstimating Platelet Mitochondrial Function in Patients with Sepsis - Platelet NMRs (part-I)
Study Typesingle timepoint
Study SummaryRelationships between platelet mitochondrial oxygen consumption rates (mOCR) and metabolites in platelets as measured by quantitative 1H-NMR metabolomics. Samples collected in ED at a single timepoint. WB and platelets isolated from the same blood samples. Comparison of mitochondrial function and metabolomics in patients with sepsis and non-sepsis ED patients
Institute
University of Michigan; University of Mississippi; University of Minnesota
DepartmentClinical Pharmacy (UMich); Emergency Medicine (UMiss)
LaboratoryStringer NMR Metabolomics Laboratory
Last NameMcHugh
First NameCora
Address428 Church St, Ann Arbor, MI, 48103, USA
EmailNMRmetabolomics@umich.edu
Phone7343530164
Submit Date2019-12-13
Num Groups2
Total Subjects23
Num Males12
Num Females11
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2020-05-26
Release Version1
Cora McHugh Cora McHugh
https://dx.doi.org/10.21228/M8FX1M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000876
Project DOI:doi: 10.21228/M8FX1M
Project Title:Estimating Platelet Mitochondrial Function in Patients with Sepsis
Project Type:Quantitative NMR Metabolomics
Project Summary:Sepsis patients and ill controls admitted to the ED had matched whole blood (WB) and isolated platelet samples collected. The control group was chosen to represent an acutely ill 127cohort of the same racial, sex, and age as the sepsis cohort. NMR was run on extracted WB and platelets to determine how the metabolome reflects mitochondrial function
Institute:University of Michigan; University of Mississippi; University of Minnesota
Department:Clinical Pharmacy (UMich); Emergency Medicine (UMiss)
Laboratory:Stringer NMR Metabolomics Laboratory
Last Name:McHugh
First Name:Cora
Address:428 Church St, Ann Arbor, MI, 48103, USA
Email:NMRmetabolomics@umich.edu
Phone:7343530164
Funding Source:GM111400, K23GM113041
Contributors:Kathleen Stringer, Mike Puskarich, Marc McCann

Subject:

Subject ID:SU001368
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:32-67
Gender:Male and female
Human Race:Caucasian (C) and African American (AA)
Human Ethnicity:non-hispanic
Human Inclusion Criteria:Sepsis: 1) Suspected or confirmed infection; 2) Any two of four criteria of systemic inflammatory response in ED(18); 3) Age ≥ 18; 4) Lactate ≥ 2.0 mmol/L; 5) Enrollment within 2 hours of initiation of quantitative resuscitation protocol. Controls: admitted to the emergency department and had no medical conditions that required chronic administration of medication expected to affect platelet function (aspirin, PGY12 inhibitors, etc)
Human Exclusion Criteria:Exclusion criteria were:1) any primary diagnosis other than sepsis; 2) established Do Not Resuscitate status; 3) transferred from another hospital with sepsis therapy already initiated; 4) cardiopulmonary resuscitation (chest compression or defibrillation) prior to enrollment; 5) patient or legal representative unable to understand and sign informed consent.

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Condition
SA094082233_17Control
SA094083233_02Control
SA094084233_06Control
SA094085233_05Control
SA094086233_33Control
SA094087233_07Control
SA094088233_18Control
SA094089233_01Control
SA094090233_11Control
SA094091233_30Control
SA094092233_34Control
SA094093233_37Control
SA094094233_39Control
SA094095233_35Control
SA094096233_27Sepsis
SA094097233_09Sepsis
SA094098233_13Sepsis
SA094099233_12Sepsis
SA094100233_03Sepsis
SA094101233_16Sepsis
SA094102233_26Sepsis
SA094103233_08Sepsis
SA094104233_40Sepsis
SA094105233_23Sepsis
SA094106233_14Sepsis
SA094107233_15Sepsis
SA094108233_20Sepsis
SA094109233_22Sepsis
SA094110233_28Sepsis
SA094111233_10Sepsis
SA094112233_38Sepsis
SA094113233_19Sepsis
SA094114233_31Sepsis
SA094115233_32Sepsis
SA094116233_25Sepsis
SA094117233_21Sepsis
SA094118233_24Sepsis
SA094119233_04Sepsis
SA094120233_29Sepsis
Showing results 1 to 39 of 39

Collection:

Collection ID:CO001363
Collection Summary:WB samples (12 mL each) were collected by direct venipuncture or from an indwelling line into K2 EDTA-containing tubes. Platelets were then isolated. centrifuged (200x gfor 6 min at room temperature).The platelet-rich plasma layer was transferred to another tube and centrifuged (4500x gfor 5 minat 4C) to pellet the platelets.The nearly cell-free plasma layer was transferred to a new tube, leaving approximately 0.25 mL of plasma in the original tube. Remaining plasma was used to resuspend the platelet pellet to produce ultra-rich plasma.
Sample Type:Platelets
Collection Method:direct venipuncture or indwelling line
Collection Frequency:once
Volumeoramount Collected:12mL
Storage Conditions:Described in summary
Collection Vials:K2 EDTA-containing Vacutainer tubes (BD 134367863; Becton-Dickinson, Franklin Lakes, NJ USA)
Additives:K2 EDTA

Treatment:

Treatment ID:TR001383
Treatment Summary:No treatment. Sepsis and non-sepsis controls had platelets isolated. Mitochondrial function was measured via mitochondrial oxygen consumption (mOCR)

Sample Preparation:

Sampleprep ID:SP001376
Sampleprep Summary:Methanol chlorform extraction of platelet pellet after 2 freeze-thaw cycles in the presence of methanol.
Sampleprep Protocol ID:Platelet Pellet MeOHCHCl3 Extraction
Sampleprep Protocol Filename:233.2.1_-_HAPS_Platelet_Pellet_MeOHCHCl3_Extraction
Processing Storage Conditions:On ice
Extraction Method:Methanol chloroform extraction
Extract Enrichment:Lyophilization
Extract Storage:-80℃
Sample Resuspension:500uL 50mM sodium phosphate buffer in D2O
Sample Spiking:4.99 mM DSS internal standard

Analysis:

Analysis ID:AN002155
Laboratory Name:University of Michigan BioNMR core
Analysis Type:NMR
Acquisition Date:04/02/2018, 04/03 /2018, 04/04/2018, 04/05/2018
Software Version:TopSpin 4.0.7
Operator Name:Larisa Yeomans, Jae Hyun Kim
Data Format:.fid
Num Factors:2
Num Metabolites:19
Units:µM

NMR:

NMR ID:NM000157
Analysis ID:AN002155
Instrument Name:Bruker 18.8 Tesla (800 MHz) NMR spectrometer ascend
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
NMR Comments:Arrayed for water saturation frequency and 90deg. pulse width for each sample
Standard Concentration:10% (~0.5mM)
Spectrometer Frequency:800 MHz
NMR Probe:Triple resonance inverse detection TCI cryoprobe
NMR Solvent:D20
NMR Tube Size:5mm
Shimming Method:Auto shim (gradient shimming)
Pulse Sequence:noesygppr1d
Water Suppression:saturation at 80 Hz induced field strength
Pulse Width:5.5ms
Offset Frequency:around -178Hz
Presaturation Power Level:80db
Chemical Shift Ref Cpd:DSS-d6
Temperature:25
Number Of Scans:128
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