Summary of Study ST001267
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 PR000852. The data can be accessed directly via it's Project DOI: 10.21228/M8JT4N This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
Study ID | ST001267 |
Study Title | Mass spectrometry-based lipidomics of oral squamous cell carcinoma tissue reveals aberrant cholesterol and glycerophospholipid metabolism |
Study Type | Case study |
Study Summary | Comparison between the lipid profile in oral squamous cell carcinoma of the tongue and healthy epithelial tissue from the contralateral side of the tongue of the same patient. |
Institute | University of Helsinki |
Department | Department of Otorhinolaryngology-Head and Neck Cancer |
Last Name | Silén |
First Name | Suvi |
Address | Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, PO Box 263, FI-00029 HUS, Helsinki, Finland |
Suvi.silen@helsinki.fi | |
Phone | NA |
Submit Date | 2019-10-09 |
Num Groups | 2 |
Total Subjects | 10 |
Num Males | 6 |
Num Females | 4 |
Raw Data Available | Yes |
Analysis Type Detail | MS(Dir. Inf.) |
Release Date | 2020-04-13 |
Release Version | 1 |
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Sample Preparation:
Sampleprep ID: | SP001343 |
Sampleprep Summary: | Frozen samples were homogenised in LC-MS grade water (LicChrosolv®): they were placed in a homogenisation bead tube and homogenised for 6 runs at 45 seconds at 6.5 m/s with 5 minutes incubation on ice in-between runs, then diluted to a concentration of 5mg/ml before being stored at -72ºC until further MS processing. MS-based lipid analysis was performed by Lipotype GmbH (Dresden, Germany). Lipids were extracted using a two-step chloroform/methanol procedure (25). Samples were spiked with internal lipid standard mixture containing: cardiolipin 16:1/15:0/15:0/15:0 (CL), ceramide 18:1;2/17:0 (Cer), diacylglycerol 17:0/17:0 (DAG), hexosylceramide 18:1;2/12:0 (HexCer), lyso-phosphatidate 17:0 (LPA), lyso-phosphatidylcholine 12:0 (LPC), lyso-phosphatidylethanolamine 17:1 (LPE), lyso-phosphatidylglycerol 17:1 (LPG), lyso-phosphatidylinositol 17:1 (LPI), lyso-phosphatidylserine 17:1 (LPS), phosphatidate 17:0/17:0 (PA), phosphatidylcholine 17:0/17:0 (PC), phosphatidylethanolamine 17:0/17:0 (PE), phosphatidylglycerol 17:0/17:0 (PG), phosphatidylinositol 16:0/16:0 (PI), phosphatidylserine 17:0/17:0 (PS), cholesterol ester 20:0 (CE), sphingomyelin 18:1;2/12:0;0 (SM), triacylglycerol 17:0/17:0/17:0 (TAG) and cholesterol D6 (Chol). After extraction, the organic phase was transferred to an infusion plate and dried in a speed vacuum concentrator. The first-step dry extract was re-suspended in 7.5 mM ammonium acetate in chloroform/methanol/propanol (1:2:4, V:V) and the 2nd step dry extract resuspended in 33% ethanol solution of methylamine in chloroform/methanol (0.003:5:1; V:V). All liquid handling steps were performed using Hamilton Robotics STARlet robotic platform with the Anti Droplet Control feature for organic solvents pipetting. |