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MB Sample ID: SA151273

Local Sample ID:1
Subject ID:SU001719
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

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Subject:

Subject ID:SU001719
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
1SA151273FL017695HRT1DDisease status

Collection:

Collection ID:CO001712
Collection Summary:Blood samples (~20 mL/subject in EDTA) were collected from consented male/female subjects considered at high risk for T1D during routine visits as part of the ongoing TrialNet’s Natural History Study of the Development of Type 1 Diabetes (Pathway to Prevention Study) TN-01 study (n=4). Subjects in the TN-01 study are tested semi-annually for the appearance of new or additional autoantibodies and are evaluated metabolically by oral glucose tolerance test (OGTT) to assess their progression toward clinical diagnosis of T1D. Samples from healthy subjects (n=4) were collected as part of another study approved by the IRB of the University of Miami (study number 11995-115). During sample collection, one of the four high-risk subjects exhibited signs of abnormal OGTT and was confirmed to have converted to a new-onset patient during a second OGTT and another sample collection two weeks later. Both samples were independently analyzed by multi-omics, and the averaged values for each identified feature in both samples were included in the integrative analyses as part of the high-risk group to avoid further reduction in the subject number. Samples from all subjects were divided into four equal aliquots that were individually subjected to proteomics, metabolomics, lipidomics, and transcriptomics (miRNAs) analyses (i.e., parallel quadra-omics) that were performed in collaboration with the Miami Integrative Metabolomics Research Center (lipidomics), Pacific Northwest National Laboratories (proteomics) [58], Ocean Ridge Biosciences (transcriptomics), and the Stedman Metabolomics Laboratory at Duke University Medical Center (metabolomics).
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001732
Treatment Summary:Plasma was collected from high-risk type 2 diabetes subjects and healthy controls. The methyl tert-butyl ether (MTBE) method was used for lipid extraction, followed by mass spectrometry lipid profiling with a Q-Exactive Orbitrap Liquid Chromatography-Mass Spectrometer (LC MS-MS).

Sample Preparation:

Sampleprep ID:SP001725
Sampleprep Summary:Lipids were extracted from 50 µL of plasma by adding 4 mL of methyl tert-butyl ether (MTBE) and 1.2 mL of butylated hydroxytoluene (BHT) then incubating overnight at 4°C. The following day, 1.25 mL of 0.15 M ammonium acetate was added, and the samples were centrifuged at 2,000 x g for 10 minutes at 4°C to obtain phase separation. The upper organic phase was collected and the extracted lipids equivalent to 100 µg of protein were dried in a speed vacuum concentrator. The samples were reconstituted in 50 µL of chloroform:methanol (1:1) and sonicated before analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The lipids were analyzed by LC-MS/MS using an Accela 600 HPLC and a Q Exactive Orbitrap mass spectrometer.

Combined analysis:

Analysis ID AN002687
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Accela 600
Column Thermo Acclaim 120 (150 x 2.1mm,3um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH001981
Instrument Name:Thermo Accela 600
Column Name:Thermo Acclaim 120 (150 x 2.1mm,3um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002486
Analysis ID:AN002687
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Xcalibur software. LipidSearch for data processing.
Ion Mode:POSITIVE
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