Summary of Study ST000904

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 PR000628. The data can be accessed directly via it's Project DOI: 10.21228/M8H10W This work is supported by NIH grant, U2C- DK119886.

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Study IDST000904
Study TitleMeasurement of 2-hydroxyglutarate for reproducibility project
Study SummaryMeasurement of D-2-hydroxyglutarate and comparison of peak area with glutamate
Institute
Sanford Burnham Prebys Medical Discovery Institute
Last NameScott
First NameDavid
Address10901 N. Torrey Pines Road
Emaildscott@sbpdiscovery.org
Phone858-646-3100
Submit Date2017-11-22
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2018-02-07
Release Version1
David Scott David Scott
https://dx.doi.org/10.21228/M8H10W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000628
Project DOI:doi: 10.21228/M8H10W
Project Title:Measurement of 2-hydroxyglutarate for reproducibility project
Project Summary:The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered Report describes the proposed replication plan of key experiments from IDH mutation impairs histone demethylation and results in a block to cell differentiation by Lu and colleagues, published in Nature in 2012 (Lu et al., 2012). The experiments that will be replicated are those reported in Figures 1B, 2A, 2B, 2D and 4D. Lu and colleagues demonstrated that expression of mutant forms of IDH1 or IDH2 caused global increases in histone methylation and increased levels of 2 hydroxyglutarate (Figure 1B). This was correlated with a block in differentiation (Figures 2A, B and D). This effect appeared to be mediated by the histone demethylase KDM4C (Figure 4D). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Scienceand Science Exchange, and the results of the replications will be published by eLife.
Institute:Sanford Burnham Prebys Medical Discovery Institute
Last Name:Scott
First Name:David
Address:10901 N. Torrey Pines Road, La Jolla, California, 92037, USA
Email:dscott@sbpdiscovery.org
Phone:858-646-3100

Subject:

Subject ID:SU000941
Subject Type:Animal
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Strain Details:293T cells
Species Group:Human

Factors:

Subject type: Animal; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id IDH expression
SA052957Prtcl1_Run3_IDH1mut1IDH1mut
SA052958Prtcl1_Run2_IDH1mut2IDH1mut
SA052959Prtcl1_Run4_IDH1mut1IDH1mut
SA052960Prtcl1_Run5_IDH1mut1IDH1mut
SA052961Prtcl1_Run6_IDH1mut1IDH1mut
SA052962Prtcl1_Run2_IDH1mut1IDH1mut
SA052963Prtcl1_Run3_IDH1mut2IDH1mut
SA052964Prtcl1_Run1_IDH1mut2IDH1mut
SA052965Prtcl1_Run1_IDH1mut1IDH1mut
SA052966Prtcl1_Run6_IDH1wt1IDH1wt
SA052967Prtcl1_Run3_IDH1wt2IDH1wt
SA052968Prtcl1_Run1_IDH1wt2IDH1wt
SA052969Prtcl1_Run1_IDH1wt1IDH1wt
SA052970Prtcl1_Run4_IDH1wt1IDH1wt
SA052971Prtcl1_Run2_IDH1wt1IDH1wt
SA052972Prtcl1_Run2_IDH1wt2IDH1wt
SA052973Prtcl1_Run3_IDH1wt1IDH1wt
SA052974Prtcl1_Run5_IDH1wt1IDH1wt
SA052975Prtcl2_Run4_IDH2mut1IDH2mut
SA052976Prtcl1_Run5_IDH2mut1IDH2mut
SA052977Prtcl2_Run1_IDH2mut1IDH2mut
SA052978Prtcl2_Run2_IDH2mut1IDH2mut
SA052979Prtcl2_Run3_IDH2mut1IDH2mut
SA052980Prtcl1_Run6_IDH2mut1IDH2mut
SA052981Prtcl1_Run1_IDH2mut1IDH2mut
SA052982Prtcl1_Run4_IDH2mut1IDH2mut
SA052983Prtcl1_Run3_IDH2mut2IDH2mut
SA052984Prtcl1_Run3_IDH2mut1IDH2mut
SA052985Prtcl2_Run5_IDH2mut1IDH2mut
SA052986Prtcl1_Run1_IDH2mut2IDH2mut
SA052987Prtcl1_Run2_IDH2mut2IDH2mut
SA052988Prtcl1_Run2_IDH2mut1IDH2mut
SA052989Prtcl2_Run1_IDH2wt1IDH2wt
SA052990Prtcl1_Run1_IDH2wt2IDH2wt
SA052991Prtcl1_Run1_IDH2wt1IDH2wt
SA052992Prtcl1_Run3_IDH2wt1IDH2wt
SA052993Prtcl2_Run3_IDH2wt1IDH2wt
SA052994Prtcl1_Run3_IDH2wt2IDH2wt
SA052995Prtcl2_Run2_IDH2wt1IDH2wt
SA052996Prtcl1_Run6_IDH2wt1IDH2wt
SA052997Prtcl1_Run2_IDH2wt1IDH2wt
SA052998Prtcl1_Run5_IDH2wt1IDH2wt
SA052999Prtcl2_Run5_IDH2wt1IDH2wt
SA053000Prtcl2_Run4_IDH2wt1IDH2wt
SA053001Prtcl1_Run2_IDH2wt2IDH2wt
SA053002Prtcl1_Run4_IDH2wt1IDH2wt
SA053003Prtcl2_Run3_vec1vector
SA053004Prtcl2_Run4_vec1vector
SA053005Prtcl2_Run5_vec1vector
SA053006Prtcl1_Run4_vec1vector
SA053007Prtcl1_Run3_vec1vector
SA053008Prtcl1_Run2_vec1vector
SA053009Prtcl1_Run1_vec2vector
SA053010Prtcl1_Run3_vec2vector
SA053011Prtcl1_Run1_vec1vector
SA053012Prtcl2_Run1_vec1vector
SA053013Prtcl1_Run6_vec1vector
SA053014Prtcl1_Run5_vec1vector
SA053015Prtcl2_Run2_vec1vector
Showing results 1 to 59 of 59

Collection:

Collection ID:CO000935
Collection Summary:Cells were washed x3 in cold PBS, then scraped into 80% methanol containing 20 uM L-norvaline
Collection Protocol Filename:GC-MS analysis of D-2-hydroxyglutarate
Sample Type:Adherent cultured mammalian cells

Treatment:

Treatment ID:TR000955
Treatment Summary:Cells transfected with empty vector or vector expressing wild-type or mutant isocitrate dehydrogenase (IDH1 or IDH2; mutations respectively R132H or R172K)

Sample Preparation:

Sampleprep ID:SP000948
Sampleprep Summary:Methanol/water extracts were counter-extracted with chloroform to remove non-polar metabolites, dried in a centrifugal evaporator, and derivatized in 60 ul 1:1 mix acetonitrile: MTBSTFA, with heating for 75 min at 75C

Combined analysis:

Analysis ID AN001471
Analysis type MS
Chromatography type GC
Chromatography system Shimadzu
Column Rxi-5ms
MS Type EI
MS instrument type Single quadrupole
MS instrument name Shimadzu QP2010 Plus
Ion Mode POSITIVE
Units ion counts

Chromatography:

Chromatography ID:CH001034
Instrument Name:Shimadzu
Column Name:Rxi-5ms
Chromatography Type:GC

MS:

MS ID:MS001359
Analysis ID:AN001471
Instrument Name:Shimadzu QP2010 Plus
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
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