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MB Sample ID: SA113927
| Local Sample ID: | CMH70994 |
| Subject ID: | SU001476 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 0-18 years old |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001476 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 0-18 years old |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| CMH70994 | SA113927 | FL014363 | 12 to 18 years | GROUP_DESCRIPTION |
Collection:
| Collection ID: | CO001471 |
| Collection Summary: | Postmortem pediatric human liver tissue samples were obtained through the Brain and Tissue Bank for Developmental Disorders at the University of Maryland (Baltimore, MD), the Liver Tissue Cell Distribution System (LTCDS; University of Pittsburgh and University of Minnesota), and XenoTech LLC (Lenexa, KS). The use of these tissues was classified as nonhuman subject research by the Children's Mercy Hospital Pediatric Institutional Review Board A replication set of post-mortem liver tissue samples from autopsy of fetuses (from therapeutic abortions or stillbirths) and infants was provided by the Erasmus Medical Center Tissue Bank, Sophia Children’s Hospital, Rotterdam, The Netherlands. Tissue was procured at the time of autopsy within 24 h after death and snap-frozen at −80 °C for later research use. The Erasmus Medical Center Research Ethics Board waived the need for formal ethics approval according to the Dutch Law on Medical Research in Humans. Tissue was collected when parental written informed consent for both autopsy and the explicit use of the tissue for research was present. Samples were selected based on the absence of a clinical diagnosis or medications affecting the liver (CMH and Erasmus), and tissue that was histologically normal (Erasmus). Samples were stratified into four age groups: less than one year of age (age group 1), one to less than six years (age group 2), six to less than 12 years (age group 3), and 12 to 18 years of age (age group 4). In total 98 liver samples were available for metabolomic analysis. |
| Sample Type: | Liver |
Treatment:
| Treatment ID: | TR001491 |
| Treatment Summary: | No treatment. |
Sample Preparation:
| Sampleprep ID: | SP001484 |
| Sampleprep Summary: | Experiment 1 The first experiment was completed using the first set of samples (N = 48) (referred to as “batch 1”). Metabolite extraction and detection were performed at Metabolon Inc. (Durham, NC, USA) as previously described (Evans et al., 2009). Briefly, liver samples were extracted through the automated MicroLab STAR® system (Hamilton Company, UT, USA), centrifuged, and the resulting supernatants were analyzed by UPLC-MS/MS in a positive and negative ion mode (UPLC: Waters, Milford, MA; mass spectrometer: Thermo-Finnigan LTQ, Thermo Fisher Scientific, Waltham, MA, scan range, 80–1000 m/z) and by GC-MS (Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer, scan range 50–750 m/z). The final experiment 1 metabolomic dataset comprised a total of 751 biochemicals, 478 scompounds of known identity (named biochemicals) and 273 compounds of unknown structural identity. As initial statistical analysis revealed an age-dependent effect that could not be distinguished from a tissue source-related effect, a replication set of group 1 samples was obtained through collaboration with Erasmus Medical Center/Sophia Children’s Hospital. Experiment 2 Given that the metabolomic platform changed between the first analysis and the sample set containing the replication samples, the second experiment examined the entire set of 98 samples. The same 48 samples previously processed in Experiment 1 and designated as “batch 1” above were re-analyzed on the new platform, with the results designated “batch 2”. The replication samples from Erasmus/Sophia Children’s Hospital and additional samples from CMH (N=50) are designated as “batch 3”. Following the sample extraction, the resulting extract was analyzed using a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution (Evans et al., 2014). Four methods were utilized: two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), RP/UPLC-MS/MS with negative ion mode ESI, and HILIC/UPLC-MS/MS with negative ion mode ESI. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. The final experiment 2 metabolomic dataset comprised a total of 971 biochemicals, 779 compounds of known identity (named biochemicals) and 192 compounds of unknown structural identity. |
Combined analysis:
| Analysis ID | AN002344 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Trace 1310 |
| Column | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Single quadrupole |
| MS instrument name | Thermo Trace DSQ |
| Ion Mode | UNSPECIFIED |
| Units | estimated abundances |
Chromatography:
| Chromatography ID: | CH001717 |
| Instrument Name: | Thermo Trace 1310 |
| Column Name: | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002186 |
| Analysis ID: | AN002344 |
| Instrument Name: | Thermo Trace DSQ |
| Instrument Type: | Single quadrupole |
| MS Type: | ESI |
| MS Comments: | Metabolon |
| Ion Mode: | UNSPECIFIED |
