Summary of Study ST002536
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 PR001632. The data can be accessed directly via it's Project DOI: 10.21228/M8RB05 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002536 |
| Study Title | Effectors enabling adaptation to mitochondrial complex I loss in Hürthle cell carcinoma |
| Study Type | comparison of tumor versus normal tissue |
| Study Summary | With the goal of performing RNA-seq and metabolomic profiling, a cohort of fresh frozen oncocytic (Hürthle cell) thyroid carcinoma (HCC) samples was established with confirmation of mtDNA mutation status and chromosomal copy number. This cohort contained 24 oncocytic (Hürthle cell) tumors with 18 cases having matched normal thyroid tissue. Tumor samples included 21 primary tumors comprised of 19 HCC (8 widely invasive, 11 minimally invasive) and 2 oncocytic (Hürthle cell) adenomas as well as 2 locoregional recurrences (LR) and 1 distant metastasis (DM). HCC samples were collected and stored as part of the Mass General Brigham Institutional Review Board (protocol number 2008P001466). Frozen tissue was accessed to create the cohort used in the study. |
| Institute | Broad Institute of MIT and Harvard |
| Department | Metabolomics Platform |
| Last Name | Clish |
| First Name | Clary |
| Address | 415 Main Street, Cambridge, MA, 02142, USA |
| clary@broadinstitute.org | |
| Phone | 617-714-7654 |
| Submit Date | 2023-03-30 |
| Num Groups | 2 |
| Total Subjects | tumors from 24 subjects and matched normal tissue from a subset of 18 subjects |
| Num Males | N/A |
| Num Females | N/A |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004171 | AN004172 | AN004173 | AN004174 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
| Chromatography system | Shimadzu Nexera X2 | Shimadzu Nexera X2 | Shimadzu Nexera X2 | Shimadzu Nexera X2 |
| Column | Waters Atlantis HILIC (150 x 2.1mm,3um,100Å | Phenomenex Luna NH2 (150 x 2 mm,5um;100Å) | Waters ACQUITY UPLC BEH C8 Column (2.1 mm X 100 mm,1.7 µm,130Å) | Waters ACQUITY UPLC BEH C18 Column (2.1 mm X 150 mm,1.7 µm,130Å) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Exactive Plus Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | peak area | peak area | peak area | peak area |
Chromatography:
| Chromatography ID: | CH003089 |
| Chromatography Summary: | HILIC-pos: Hydrophilic interaction liquid chromatography (HILIC) analysis of water soluble metabolites in the positive ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Atlantis HILIC (150 x 2.1mm,3um,100Å |
| Column Temperature: | 30 |
| Flow Gradient: | 0-0.5 min, isocratic 95% B; 0.5-10.5 min, gradient to 40% B; 10.5-15 min, isocratic 40% B; 15-17 min, gradient to 95% B |
| Flow Rate: | 250 uL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003090 |
| Chromatography Summary: | HILIC-neg: Hydrophilic interaction liquid chromatography (HILIC) analysis of water soluble metabolites in the negative ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Phenomenex Luna NH2 (150 x 2 mm,5um;100Å) |
| Column Temperature: | 30 |
| Flow Gradient: | 0-10 min, gradient from 90% B to 0% B; 10-12 min, isocratic 0% B; 12-14 min, gradient from 0% B to 90% B |
| Flow Rate: | 400 uL/min |
| Solvent A: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide |
| Solvent B: | 75% methanol/25% acetonitrile; 10 mM ammonium hydroxide |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003091 |
| Chromatography Summary: | C8-pos: Reversed-phase C8 chromatography analysis of polar and nonpolar lipids in the positive ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters ACQUITY UPLC BEH C8 Column (2.1 mm X 100 mm,1.7 µm,130Å) |
| Column Temperature: | 40 |
| Flow Gradient: | 0-1 min, isocratic 20% B; 1-3 min, gradient to 80% B; 3-10 min, gradient to 100% B; 10-13 min, isocratic 100% B; 13-14 min, gradient to 20% B |
| Flow Rate: | 450 uL/min |
| Solvent A: | 95% water/5% methanol; 0.1% formic acid; 10 mM ammonium acetate |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003092 |
| Chromatography Summary: | C18-neg: Reversed-phase C18 chromatography analysis of compounds of intermediate polarity in the negative ionization mode |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters ACQUITY UPLC BEH C18 Column (2.1 mm X 150 mm,1.7 µm,130Å) |
| Column Temperature: | 45 |
| Flow Gradient: | 0-3 min, isocratic 20% B; 3-15 min, gradient to 100% B; 15-18 min, isocratic 100% B; 18-19 min, gradient to 20% B |
| Flow Rate: | 450 uL/min |
| Solvent A: | 100% water; 0.01% formic acid |
| Solvent B: | 100% acetonitrile; 0.01% acetic acid |
| Chromatography Type: | Reversed phase |
