|
| Status |
Public on Oct 16, 2019 |
| Title |
TS603H1 |
| Sample type |
genomic |
| |
|
| Source name |
grade III oligodendroglioma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TS603
cell type: Glioma stem cells
genotype: IDH1 mutant
stress: hypoxia (H)
|
| 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 |
|
