Summary of Study ST000302

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.

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Study IDST000302
Study TitleIsocitrate dehydrogenase-1/Glioma Fluxomics Study
Study SummaryTumor neurospheres were grown in culture until ~90% confluent. Media was changed to contain 1mM acetate. After 24h, 0h time points were collected and media was changed on all other cells to 1mM 13C-acetate containing media. Cells were then collected at their various time points, 1, 3, 24, 48, or 72 hours. Cells were collected into 15mL tubes, spun down at 100xg for 1min and media aspirated. Pellet was washed (not resuspended) in 150mM ammonium acetate. This was then aspirated off and the cells snap frozen and stored at -80C until all time points complete to ship on dry ice. 0h, 1h, and 3h A, B, and C samples will have gTn by HILIC + TCA by GCMS done on them, while 0h, 1h, and 3h D, E, and F will have FAMES and DG & PC analysis done on them. 24h, 48h, and 72h A, B, and C samples will have FAMES analysis done on them.
Institute
University of Michigan
DepartmentBiomedical Research Core Facilities
LaboratoryMetabolomics core
Last NameKachman
First NameMaureen
Address6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Emailmkachman@med.umich.edu
Phone(734) 232-8175
Submit Date2015-03-24
Num Groups6
Total Subjects54
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailGC-MS/LC-MS
Release Date2016-06-18
Release Version1
Maureen Kachman Maureen Kachman
https://dx.doi.org/10.21228/M8688J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU000322
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 Cell line Labelint time (hours)
SA013636S00017834pLKO 0
SA013637S00017833pLKO 0
SA013638S00017837pLKO 0
SA013639S00017838pLKO 0
SA013640S00017835pLKO 0
SA013641S00017836pLKO 0
SA013642S00017847pLKO 1
SA013643S00017845pLKO 1
SA013644S00017848pLKO 1
SA013645S00017846pLKO 1
SA013646S00017850pLKO 1
SA013647S00017849pLKO 1
SA013648S00017870pLKO 24
SA013649S00017871pLKO 24
SA013650S00017869pLKO 24
SA013651S00017858pLKO 3
SA013652S00017859pLKO 3
SA013653S00017862pLKO 3
SA013654S00017857pLKO 3
SA013655S00017861pLKO 3
SA013656S00017860pLKO 3
SA013657S00017876pLKO 48
SA013658S00017875pLKO 48
SA013659S00017877pLKO 48
SA013660S00017881pLKO 72
SA013661S00017882pLKO 72
SA013662S00017883pLKO 72
SA013663S00017841shIDH1 0
SA013664S00017839shIDH1 0
SA013665S00017842shIDH1 0
SA013666S00017840shIDH1 0
SA013667S00017843shIDH1 0
SA013668S00017844shIDH1 0
SA013669S00017853shIDH1 1
SA013670S00017854shIDH1 1
SA013671S00017856shIDH1 1
SA013672S00017852shIDH1 1
SA013673S00017851shIDH1 1
SA013674S00017855shIDH1 1
SA013675S00017872shIDH1 24
SA013676S00017874shIDH1 24
SA013677S00017873shIDH1 24
SA013678S00017864shIDH1 3
SA013679S00017868shIDH1 3
SA013680S00017865shIDH1 3
SA013681S00017866shIDH1 3
SA013682S00017863shIDH1 3
SA013683S00017867shIDH1 3
SA013684S00017879shIDH1 48
SA013685S00017880shIDH1 48
SA013686S00017878shIDH1 48
SA013687S00017886shIDH1 72
SA013688S00017885shIDH1 72
SA013689S00017884shIDH1 72
Showing results 1 to 54 of 54

Collection:

Collection ID:CO000316
Collection Summary:-
Sample Type:Cultured cells

Treatment:

Treatment ID:TR000336
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP000330
Sampleprep Summary:-
Sampleprep Protocol Filename:Fluxomics_analysis_protocol-2015-03-11.docx

Combined analysis:

Analysis ID AN000480 AN000481
Analysis type MS MS
Chromatography type HILIC GC
Chromatography system Agilent 1260 Agilent 7890A
Column Phenomenex Luna NH2 (150 x 1mm,3um) Agilent DB5-MS (30m × 0.25mm, 0.25um)
MS Type ESI EI
MS instrument type QTOF Single quadrupole
MS instrument name Agilent 6520B QTOF Agilent 5975C
Ion Mode NEGATIVE POSITIVE
Units Area Area

Chromatography:

Chromatography ID:CH000343
Chromatography Summary:HILIC-MS
Methods Filename:QTOF-002-HILIC-35min-1mm.m.zip
Instrument Name:Agilent 1260
Column Name:Phenomenex Luna NH2 (150 x 1mm,3um)
Chromatography Type:HILIC
  
Chromatography ID:CH000344
Chromatography Summary:GCMS(FAMES)
Methods Filename:BROWN141008.M
Instrument Name:Agilent 7890A
Column Name:Agilent DB5-MS (30m × 0.25mm, 0.25um)
Flow Rate:0.075 ml/min
Solvent A:100% water; 5 mM ammonium acetate, pH 9.9
Solvent B:100% acetonitrile
Chromatography Type:GC

MS:

MS ID:MS000420
Analysis ID:AN000480
Instrument Name:Agilent 6520B QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Analysis Protocol File:Fluxomics_analysis_protocol-2015-03-11.docx
  
MS ID:MS000421
Analysis ID:AN000481
Instrument Name:Agilent 5975C
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
Analysis Protocol File:Fluxomics_analysis_protocol-2015-03-11.docx
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