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Series GSE34387 Query DataSets for GSE34387
Status Public on May 22, 2013
Title Oncogenic SDH mutation underlies global epigenomic instability in gastrointestinal stromal tumor
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary We have discovered a striking connection between mitochondrial dysfunction and epigenomic instability, manifested by global biallelic DNA cytosine 5-methylation and loss of 5-hydroxymethycytosine within succinate dehydrogenase (SDH)-null gastrointestinal stromal tumors (GIST) relative to those bearing KIT or PDGFRA tyrosine kinase driver mutations. The duality of Krebs versus kinase molecular and epigenomic profiles in GIST provides compelling evidence linking mitochondrial process to nuclear structure and function and underscores an essential role for succinate metabolism in the maintenance of epigenomic programming and tumor suppression.
 
Overall design Illumina GoldenGate Methylation Cancer Panel I: Bisulfite-converted DNA from 144 samples were analyzed with the Illumina GoldenGate Methylation Cancer Panel I array.
Illumina HumanMethylation450 BeadChip: Bisulfite-converted gDNAs from 76 samples were analyzed with the Illumina 450K Infinium Methylation assay.
 
Contributor(s) Killian JK, Kim SY, Miettinen M, Smith C, Tsokos M, Quezado M, Smith WI, Jahromi M, Walker RL, Lasota J, Wang ZF, Jones L, Waterfall JJ, Zhu YJ, Schiffman JD, O’Sullivan MJ, Stratakis C, Helman L, Meltzer PS
Citation(s) 23550148
Submission date Dec 12, 2011
Last update date Mar 22, 2019
Contact name Yuelin Jack Zhu
E-mail(s) zhujack@mail.nih.gov
Phone (240)760-7439
Organization name NCI
Department Genetics Branch, Center for Cancer Research
Lab Dr. Paul Meltzer's Lab
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (2)
GPL9183 Illumina GoldenGate Methylation Cancer Panel I
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (220)
GSM847956 geo_811 lymphnode benign reactive 1
GSM847957 geo_810 lymphnode benign reactive 2
GSM847958 geo_813 lymphnode benign reactive 3
Relations
BioProject PRJNA149587

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE34387_GEO_GIST_120211_Matrix_signal_intensities.txt.gz 2.4 Mb (ftp)(http) TXT
GSE34387_GEO_GIST_120211_processed_matrix.txt.gz 1.5 Mb (ftp)(http) TXT
GSE34387_GSM1337183-GSM1337258_non-normalized.txt.gz 172.7 Mb (ftp)(http) TXT
GSE34387_RAW.tar 183.1 Mb (http)(custom) TAR
Processed data included within Sample table
Processed data are available on Series record
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