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 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000852 |
| Project DOI: | doi: 10.21228/M8JT4N |
| Project Title: | Mass spectrometry-based lipidomics of oral squamous cell carcinoma tissue reveals aberrant cholesterol and glycerophospholipid metabolism |
| Project Type: | Case study |
| Project 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 |
| Institute: | University of Helsinki |
| Department: | Department of Otorhinolaryngology-Head and Neck Cancer |
| Last Name: | Silén |
| First Name: | Suvi |
| Address: | Haartmaninkatu 3, Helsinki, Uusimaa, 00018, Finland |
| Email: | Suvi.silen@helsinki.fi |
| Phone: | NA |
Subject:
| Subject ID: | SU001335 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 24-78 |
| Gender: | Male and female |
| Human Ethnicity: | caucasian |
| Human Inclusion Criteria: | tumour has not yet been treated with surgery, radiotherapy or chemotherapy; primary tumour |
| Human Exclusion Criteria: | concurrent other tumour |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Condition |
|---|---|---|
| SA092065 | Healthy9 | control |
| SA092066 | Healthy5 | control |
| SA092067 | Healthy10 | control |
| SA092068 | Healthy1 | control |
| SA092069 | Healthy2 | control |
| SA092070 | Healthy8 | control |
| SA092071 | Healthy3 | control |
| SA092072 | Healthy7 | control |
| SA092073 | Healthy4 | control |
| SA092074 | Healthy6 | control |
| SA092055 | OSCC7 | OSCC |
| SA092056 | OSCC1 | OSCC |
| SA092057 | OSCC8 | OSCC |
| SA092058 | OSCC9 | OSCC |
| SA092059 | OSCC10 | OSCC |
| SA092060 | OSCC5 | OSCC |
| SA092061 | OSCC6 | OSCC |
| SA092062 | OSCC2 | OSCC |
| SA092063 | OSCC4 | OSCC |
| SA092064 | OSCC3 | OSCC |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO001329 |
| Collection Summary: | Samples were collected in the operating theatre prior to the bulk tumour excision, and were washed in PBS before being snap-frozen using dry ice-ethanol slush. They were then stored at -72 Celsius |
| Sample Type: | Tongue tissue |
| Storage Conditions: | Described in summary |
| Collection Vials: | cryotube |
| Storage Vials: | cryotube |
Treatment:
| Treatment ID: | TR001350 |
| Treatment Summary: | Not applicable |
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. |
Chromatography:
| Chromatography ID: | CH001536 |
| Instrument Name: | none |
| Column Name: | none |
| Chromatography Type: | None (Direct infusion) |
Analysis:
| Analysis ID: | AN002104 |
| Analysis Type: | MS |
| Chromatography ID: | CH001536 |
| Num Factors: | 2 |
| Num Metabolites: | 1370 |
| Units: | pmol |
