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
| Study ID | ST000397 |
| Study Title | Long-term neural and physiological phenotyping of a single human |
| Study Type | Longitudinal |
| Study 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 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2016-05-11 |
| Total Subjects | 1 |
| Publications | doi: 10.1038/ncomms9885 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | peg |
| Analysis Type Detail | GC-MS |
| Release Date | 2016-06-18 |
| Release Version | 2 |
| Release Comments | Updated study design factors |
Select appropriate tab below to view additional metadata details:
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: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Data |
|---|---|---|
| SA019059 | 140421ajlsa20_1 | 1 |
| SA019060 | 140421ajlsa10_1 | 1 |
| SA019061 | 140421ajlsa36_1 | 1 |
| SA019062 | 140421ajlsa11_1 | 1 |
| SA019063 | 140421ajlsa07_1 | 1 |
| SA019064 | 140421ajlsa26_1 | 1 |
| SA019065 | 140421ajlsa48_1 | 1 |
| SA019066 | 140421ajlsa39_2 | 1 |
| SA019067 | 140421ajlsa29_1 | 1 |
| SA019068 | 140421ajlsa33_1 | 1 |
| SA019069 | 140421ajlsa34_1 | 1 |
| SA019070 | 140421ajlsa14_1 | 1 |
| SA019071 | 140421ajlsa01_1 | 1 |
| SA019072 | 140421ajlsa12_1 | 1 |
| SA019073 | 140421ajlsa37_1 | 1 |
| SA019074 | 140421ajlsa30_1 | 1 |
| SA019075 | 140421ajlsa13_1 | 1 |
| SA019076 | 140421ajlsa08_1 | 1 |
| SA019077 | 140421ajlsa41_1 | 1 |
| SA019078 | 140421ajlsa45_1 | 1 |
| SA019079 | 140421ajlsa21_1 | 1 |
| SA019080 | 140421ajlsa47_1 | 1 |
| SA019081 | 140421ajlsa35_1 | 1 |
| SA019082 | 140421ajlsa16_1 | 1 |
| SA019083 | 140421ajlsa23_1 | 1 |
| SA019084 | 140421ajlsa27_1 | 1 |
| SA019085 | 140421ajlsa17_1 | 1 |
| SA019086 | 140421ajlsa38_3 | 1 |
| SA019087 | 140421ajlsa18_1 | 1 |
| SA019088 | 140421ajlsa28_1 | 1 |
| SA019089 | 140421ajlsa24_1 | 1 |
| SA019090 | 140421ajlsa44_1 | 1 |
| SA019091 | 140421ajlsa40_2 | 1 |
| SA019092 | 140421ajlsa02_1 | 1 |
| SA019093 | 140421ajlsa03_1 | 1 |
| SA019094 | 140421ajlsa32_1 | 1 |
| SA019095 | 140421ajlsa15_1 | 1 |
| SA019096 | 140421ajlsa09_1 | 1 |
| SA019097 | 140421ajlsa25_1 | 1 |
| SA019098 | 140421ajlsa43_1 | 1 |
| SA019099 | 140421ajlsa31_1 | 1 |
| SA019100 | 140421ajlsa46_1 | 1 |
| SA019101 | 140421ajlsa42_1 | 1 |
| SA019102 | 140421ajlsa19_1 | 1 |
| SA019103 | 140421ajlsa22_1 | 1 |
| SA019104 | 140421ajlsa04_1 | 1 |
| SA019105 | 140421ajlsa05_1 | 1 |
| SA019106 | 140421ajlsa06_1 | 1 |
| 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 |
