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Sample GSM4120584 Query DataSets for GSM4120584
Status Public on Oct 16, 2019
Title BT142N2
Sample type genomic
 
Source name grade III oligoastrocytoma
Organism Homo sapiens
Characteristics cell line: BT142
cell type: Glioma stem cells
genotype: IDH1 mutant
stress: normoxia (N)
Treatment protocol Cell lines were grown either in normoxia (N) or hypoxia( H) for at least 3 days before collecting.
Growth protocol Cells were seeded in DMEM F12 media supplemented with N2, EGF, FGF and Heparin sulphate for 3 days.
Extracted molecule genomic DNA
Extraction protocol DNA methylation of cultured cells was performed using Infinium EPIC 850 array
Label Cy3, Cy5
Label protocol Standard Illumina protocol
 
Hybridization protocol Standard Illumina protocol
Scan protocol Standard Illumina protocol
Data processing DNA methylation of cultured cells was performed using Infinium EPIC array. We performed noob (Normal-exponential convolution using out-of-band probes) background correction (37) and dye bias correction using the minfi package (38). The DNA methylation score for each locus is presented as a beta ( ) value ( = (M/(M+U)) in which M and U indicate the mean methylated and unmethylated signal intensities for each locus, respectively. -values range from zero to one, with scores of zero indicating no DNA methylation and scores of one indicating complete DNA methylation. A detection p-value also accompanies each data point and compares the signal intensity difference between the analytical probes and a set of negative control probes on the array. Any data point with a corresponding p-value greater than 1x10-16 is deemed not to be statistically significantly different from background and was thus masked as NA . The genomic location of the EPIC probes was classified into those within CpG islands (CGI), in CGI shores (4kb regions flanking CGIs), or in open seas (> 4kb to the nearest CGIs) using UCSC genome table browser (hg38) CGI genomic annotation.
 
Submission date Oct 15, 2019
Last update date Oct 16, 2019
Contact name Mioara Larion
E-mail(s) mioara.larion@nih.gov
Phone 2407606825
Organization name National Institutes of Health
Department NCI, CCR
Lab Neuro-Oncology Branch
Street address 37 Convent Drive, Building 37
City Bethesda
State/province Maryland
ZIP/Postal code 20893
Country USA
 
Platform ID GPL21145
Series (2)
GSE138865 DNA Methylation of BT142 and TS603 cell lines
GSE138873 Metabolic Reprogramming Associated with Aggressiveness Occurs in the G-CIMP-High Molecular Subtypes of IDH1mut Lower Grade Gliomas

Data table header descriptions
ID_REF
VALUE normalized Average Beta
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
cg09835024 0.051273 0
cg14361672 0.884874 0
cg12950382 0.888634 0
cg02115394 0.0914872 0
cg12480843 0.0279588 0
cg26724186 0.92568 0
cg00617867 0.968843 0
cg13773083 0.321555 0
cg17236668 0.957077 0
cg19607165 0.888192 0
cg08770523 0.0267156 0
cg24040570 0.0343295 0
cg24652288 0.886236 0
cg09387925 0.0173507 0
cg01675618 0.0408141 0
cg11947782 0.984919 0
cg11945228 0.0165328 0
cg21650422 0.0274925 0
cg08360726 0.90779 0
cg05738196 0.139953 0

Total number of rows: 865859

Table truncated, full table size 18683 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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