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
Email	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

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Sample Preparation:

Sampleprep ID:	SP002642
Sampleprep Summary:	Frozen tissues were weighed and homogenized in 4 volumes of water (4 µL of water/mg tissue, 4°C) using a bead beater (TissueLyser II, QIAGEN; Germantown, MD). Tissue homogenates were aliquoted to prepare extracts for four different LC-MS methods: HILIC-pos: 10 µL of each tissue homogenate was extracted using 90 µL of acetonitrile/methanol/formic acid (74.9:24.9:0.2 v/v/v) containing stable isotope-labeled internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. HILIC-neg: 30 µL of each tissue homogenate was extracted using 120 µL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C8-pos: 10 µL of each tissue homogenate was extracted using 190 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL). The samples were centrifuged (10 min, 9,000 x g, ambient temperature), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C18-neg: 30 µL of each tissue homogenate was extracted using 90 µL of methanol containing 15R-15-methyl PGA2, 15S-15-methyl PGD2, 15S-15-methyl PGE1, 15S-15-methyl PGE2, and 15R-15-methyl PGF2alpha as an internal standards (Cayman Chemical Co.; Ann Arbor, MI). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts.

Sampleprep ID:

SP002642

Sampleprep Summary:

Frozen tissues were weighed and homogenized in 4 volumes of water (4 µL of water/mg tissue, 4°C) using a bead beater (TissueLyser II, QIAGEN; Germantown, MD). Tissue homogenates were aliquoted to prepare extracts for four different LC-MS methods: HILIC-pos: 10 µL of each tissue homogenate was extracted using 90 µL of acetonitrile/methanol/formic acid (74.9:24.9:0.2 v/v/v) containing stable isotope-labeled internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. HILIC-neg: 30 µL of each tissue homogenate was extracted using 120 µL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C8-pos: 10 µL of each tissue homogenate was extracted using 190 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL). The samples were centrifuged (10 min, 9,000 x g, ambient temperature), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C18-neg: 30 µL of each tissue homogenate was extracted using 90 µL of methanol containing 15R-15-methyl PGA2, 15S-15-methyl PGD2, 15S-15-methyl PGE1, 15S-15-methyl PGE2, and 15R-15-methyl PGF2alpha as an internal standards (Cayman Chemical Co.; Ann Arbor, MI). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts.