Summary of Study ST000199
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 PR000154. The data can be accessed directly via it's Project DOI: 10.21228/M8688J This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000199 |
| Study Title | IDH1 and Glioma knockdown idh1 (part II) |
| Study Summary | Tumor neurospheres were grown in culture until 90% confluent. To collect cells, cells were filtered through 0.45um nylon filters (Fischer Sci 099029) that were prewashed with methanol and ultrapure water using a microanalytical glass filter holder (Fisher Sci 09753E). The cells were filtered through filtration apparatus, then washed with 1mL of distilled water very quickly. Filter paper is taken immediatedly with tweezers and plunged cell side down into 6-well plate filled with liquid nitrogen placed on dry ice. Plate is wrapped in aluminum foil and stored at -80C before the liquid nitrogen evaporates. Samples are shipped on dry ice |
| Institute | University of Michigan |
| Department | Biomedical Research Core Facilities |
| Laboratory | Metabolomics core |
| Last Name | Kachman |
| First Name | Maureen |
| Address | 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 |
| mkachman@umich.edu | |
| Submit Date | 2015-06-10 |
| Num Groups | 2 |
| Total Subjects | 10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Uploaded File Size | 16 M |
| Analysis Type Detail | LC-MS |
| Release Date | 2015-12-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000154 |
| Project DOI: | doi: 10.21228/M8688J |
| Project Title: | Isocitrate dehydrogenase-1 and Glioma Studies |
| Project Summary: | Dr. Stegh will define the role of a novel glioma oncoprotein, termed isocitrate dehydrogenase-1 (IDH1), in driving progression and therapy resistance of glioblastoma (GBM). Understanding the molecular basis of the therapy refractoriness of GBM is one of the most important areas of glioma research.IDH1 is a critical enzyme of the citric acid cycle (CAC) and is a master regulator of metabolism. Building on his preliminary studies, Dr. Stegh will molecularly characterize the precise mechanism, by which IDH1 protects glioma cells from therapy-induced cell death using glioma cell and mouse models. To target IDH1 signaling in GBM, he will leverage these model systems and mechanistical knowledge to develop and preclinically characterize RNA interference RNAi-based nanomaterials. He will generate RNAi-functionalized spherical nucleic acids (SNAs) that neutralize IDH1 expression in established gliomas. Due to the negative charge of the RNA backbone, however, siRNA oligonucleotides have many downsides, such as they trigger auto-immune responses, and cannot cross the blood-brain-barrier (BBB). In contrast, SNAs are able to transverse cellular membranes, do not require the use of toxic auxiliary reagents, and accumulate in cells and intracranial tumors very effectively. They also exhibit extraordinary stability in physiological environments, cross the BBB, are highly resistant to nuclease degradation, and thus, can move through biological fluids and avoid being destroyed as “foreign materials.” Dr. Stegh proposes to preclinically evaluate these IDH1-targeting nanoconjugates to provide a fundamentally novel treatment option of patients diagnosed with GBM, and will aid in successfully implementing RNAi-based therapies into neuro-oncological practice. |
| Institute: | Northwestern University |
| Department: | Neurology |
| Laboratory: | Stegh Lab |
| Last Name: | Stegh |
| First Name: | Alexander |
| Address: | Evanston, IL |
| Email: | a-stegh@northwestern.edu |
| Phone: | 312-503-2879 |
Subject:
| Subject ID: | SU000218 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Knockdown of IDH1 |
|---|---|---|
| SA010025 | S00014999 | n/a |
| SA010026 | S00015002 | n/a |
| SA010027 | S00015003 | n/a |
| SA010028 | S00015001 | n/a |
| SA010029 | S00015000 | n/a |
| SA010030 | S00015007 | yes |
| SA010031 | S00015008 | yes |
| SA010032 | S00015005 | yes |
| SA010033 | S00015004 | yes |
| SA010034 | S00015006 | yes |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO000206 |
| Collection Summary: | - |
| Sample Type: | Cells, Cultured |
Treatment:
| Treatment ID: | TR000226 |
Sample Preparation:
| Sampleprep ID: | SP000220 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | Acyl-carnitines_analysis_protocol-CR-MK-20150528.docx |
Combined analysis:
| Analysis ID | AN000301 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1200 |
| Column | Waters Acquity HSS T3 (50 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ |
| Ion Mode | POSITIVE |
| Units | pmol/µg protein |
Chromatography:
| Chromatography ID: | CH000222 |
| Methods ID: | AQM050 |
| Methods Filename: | QM-004-Xbridg2mm_ACar+_MRM-Insert.m.zip |
| Instrument Name: | Agilent 1200 |
| Column Name: | Waters Acquity HSS T3 (50 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000250 |
| Analysis ID: | AN000301 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Acquisition Parameters File: | QM-004-Xbridg2mm_ACar+_MRM-Insert.m.zip |
| Processing Parameters File: | EX00311-acyl-carnitines-quant.m.zip |
