Summary of study ST000397

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 PR000310. The data can be accessed directly via it's Project DOI: 10.21228/M8B602 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000397
Study TitleLong-term neural and physiological phenotyping of a single human
Study TypeLongitudinal
Study SummaryThe dynamics of human brain function are increasingly well understood at the short timescale of seconds/minutes (for example, through studies of learning) and the long timescale of years/decades (for example, through studies of development andageing), but almost nothing is known about how the human brainfunction varies across the range of days to months. This is a critical gap, because major psychiatric disorders show large fluctuations in brain function over this timescale. However, the kind of dense longitudinal phenotyping that is necessary to understand this question is extremely challenging with healthy human volunteers,who are unlikely to be sufficiently motivated to sustain frequent participation in a study over a long period. For this reason, the participation of motivated experimenters can be uniquely useful for demanding longitudinal studies. We investigated the long-range dynamics of brain function andtheir relation to a broad set of psychological and biological variables in a single healthy human (author R.A.P.) over the course of 532 days (along with several follow-up visits), representing one of the most intensive biological characterizations of a single individual ever performed (referred to hereafter as the MyConnectomestudy). The study was designed to measure the broadest possible range of human phenotypes (the phenome’3,4) to allow the widespread assessment of relations between psychological, neural and metabolic function. The results of the present study demonstrate that healthy brain function shows rich dynamics over the course of 18 months, and that these dynamics are paralleled by ongoing fluctuations in psychological and physiological function as observed in behaviour,gene expression and metabolomic measurements. These findings provide a proof of concept for the dynamic longitudinal phenotyping of individuals, which we propose will be crucial togain a better understanding of the substantial fluctuations in psychological and neural function in individuals with major psychiatric disorders.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2016-05-11
Total Subjects1
Publicationsdoi: 10.1038/ncomms9885
Raw Data AvailableYes
Raw Data File Type(s).peg
Analysis Type DetailGC-MS
Release Date2016-06-18
Release Version2
Release CommentsUpdated study design factors
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8B602
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000310
Project DOI:doi: 10.21228/M8B602
Project Title:Long-term neural and physiological phenotyping of a single human
Project Type:Longitudinal
Project Summary:The dynamics of human brain function are increasingly well understood at the short timescale of seconds/minutes (for example, through studies of learning) and the long timescale of years/decades (for example, through studies of development andageing), but almost nothing is known about how the human brainfunction varies across the range of days to months. This is a critical gap, because major psychiatric disorders show large fluctuations in brain function over this timescale. However, the kind of dense longitudinal phenotyping that is necessary to understand this question is extremely challenging with healthy human volunteers,who are unlikely to be sufficiently motivated to sustain frequent participation in a study over a long period. For this reason, the participation of motivated experimenters can be uniquely useful for demanding longitudinal studies. We investigated the long-range dynamics of brain function andtheir relation to a broad set of psychological and biological variables in a single healthy human (author R.A.P.) over the course of 532 days (along with several follow-up visits), representing one of the most intensive biological characterizations of a single individual ever performed (referred to hereafter as the MyConnectomestudy). The study was designed to measure the broadest possible range of human phenotypes (the phenome’3,4) to allow the widespread assessment of relations between psychological, neural and metabolic function. The results of the present study demonstrate that healthy brain function shows rich dynamics over the course of 18 months, and that these dynamics are paralleled by ongoing fluctuations in psychological and physiological function as observed in behaviour,gene expression and metabolomic measurements. These findings provide a proof of concept for the dynamic longitudinal phenotyping of individuals, which we propose will be crucial togain a better understanding of the substantial fluctuations in psychological and neural function in individuals with major psychiatric disorders.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:NIH U24DK097154
Publications:doi: 10.1038/ncomms9885

Subject:

Subject ID:SU000418
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Data
SA019059140421ajlsa20_11
SA019060140421ajlsa10_11
SA019061140421ajlsa36_11
SA019062140421ajlsa11_11
SA019063140421ajlsa07_11
SA019064140421ajlsa26_11
SA019065140421ajlsa48_11
SA019066140421ajlsa39_21
SA019067140421ajlsa29_11
SA019068140421ajlsa33_11
SA019069140421ajlsa34_11
SA019070140421ajlsa14_11
SA019071140421ajlsa01_11
SA019072140421ajlsa12_11
SA019073140421ajlsa37_11
SA019074140421ajlsa30_11
SA019075140421ajlsa13_11
SA019076140421ajlsa08_11
SA019077140421ajlsa41_11
SA019078140421ajlsa45_11
SA019079140421ajlsa21_11
SA019080140421ajlsa47_11
SA019081140421ajlsa35_11
SA019082140421ajlsa16_11
SA019083140421ajlsa23_11
SA019084140421ajlsa27_11
SA019085140421ajlsa17_11
SA019086140421ajlsa38_31
SA019087140421ajlsa18_11
SA019088140421ajlsa28_11
SA019089140421ajlsa24_11
SA019090140421ajlsa44_11
SA019091140421ajlsa40_21
SA019092140421ajlsa02_11
SA019093140421ajlsa03_11
SA019094140421ajlsa32_11
SA019095140421ajlsa15_11
SA019096140421ajlsa09_11
SA019097140421ajlsa25_11
SA019098140421ajlsa43_11
SA019099140421ajlsa31_11
SA019100140421ajlsa46_11
SA019101140421ajlsa42_11
SA019102140421ajlsa19_11
SA019103140421ajlsa22_11
SA019104140421ajlsa04_11
SA019105140421ajlsa05_11
SA019106140421ajlsa06_11
Showing results 1 to 48 of 48

Collection:

Collection ID:CO000412
Collection Summary:The whole blood was separated using Ficoll gradient.
Collection Protocol Filename:StudyDesign_RussPoldrack_04.10.14.pdf
Sample Type:Blood
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000432
Treatment Summary:These are samples from the same individual taken over the course of 18 months. We are interested in comparing these results to other measurements from the same individual, including RNA-seq and brain imaging.
Treatment Protocol Filename:StudyDesign_RussPoldrack_04.10.14.pdf

Sample Preparation:

Sampleprep ID:SP000425
Sampleprep Summary:1. Switch on bath to pre-cool at –20°C (±2°C validity temperature range) 2. Gently rotate or aspirate the blood samples for about 10s to obtain a homogenised sample. 3. Aliquot 30μl of plasma sample to a 1.0 mL extraction solution. The extraction solution has to be prechilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. 4. Vortex the sample for about 10s and shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. If you are using more than one sample, keep the rest of the sample on ice (chilled at <0°C with sodium chloride). 5. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 450μL portions of the supernatant. One for analysis and one for a backup sample. Store the backup aliquot in -20°C freezer. 7. Evaporate one 450μL aliquots of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. The dried aliquot is then re-suspended with 450 μL 50% acetonitrile (degassed as given above). 9. Centrifuged for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 10. Remove supernatant to a new Eppendorf tube. 11. Evaporate the supernatant to dryness in the Labconco Centrivap cold trap concentrator. 12. Submit to derivatization.
Sampleprep Protocol Filename:SOP_blood-GCTOF-11082012.pdf

Combined analysis:

Analysis ID AN000634
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Restek Corporation Rtx-5Sil MS
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units counts

Chromatography:

Chromatography ID:CH000459
Methods Filename:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf
Instrument Name:Agilent 6890N
Column Name:Restek Corporation Rtx-5Sil MS
Column Pressure:7.7 PSI
Column Temperature:50-330C
Flow Rate:1 ml/min
Injection Temperature:50 C ramped to 250 C by 12 C/s
Sample Injection:0.5 uL
Oven Temperature:50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min
Transferline Temperature:230C
Washing Buffer:Ethyl Acetate
Sample Loop Size:30 m length x 0.25 mm internal diameter
Randomization Order:Excel generated
Chromatography Type:GC

MS:

MS ID:MS000567
Analysis ID:AN000634
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Mode:POSITIVE
Ion Source Temperature:250 C
Ionization Energy:70 eV
Mass Accuracy:Nominal
Source Temperature:250 C
Scan Range Moverz:85-500 Da
Scanning Cycle:17 Hz
Scanning Range:85-500 Da
Skimmer Voltage:1850 V
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