|
| Status |
Public on Dec 13, 2023 |
| Title |
glioma_Primary [TCGA-TQ-A7RR-TP-01M-450-6C850C] |
| Sample type |
genomic |
| |
|
| Source name |
TCGA-TQ-A7RR
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age_diagnosis_years: 38
surgical_interval_mo: NULL
who.classification.2021: Astrocytoma, IDH-mutant (WHO grade 2)
recurrent_status: Primary
idh_status: IDHmut
codel_status: noncodel
tcga.subtype: G-CIMP-high
heidelberg_meth_subtype: astrocytoma
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and purified at each institution following standard protocols that ensure high quality DNA.
|
| Label |
Cy3/Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
TCGA-TQ-A7RR-TP-01M-450-6C850C
|
| Data processing |
The raw DNA methylation intensity data files (IDAT) were processed with the minfi package. We performed noob (Normal-exponential convolution using out-of-band probes) background correction and dye bias correction using the minfi package (v 1.36.0). The DNA methylation value for each locus is presented as a beta (β) value (β = (M/(M+U)) in which M and U indicate the mean methylated and unmethylated signal intensities for each locus, respectively. β-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 1E-4 is deemed not to be statistically significantly different from background and was thus masked as “NA”.
matrix processed value definition: Average Beta
|
| |
|
| Submission date |
Nov 22, 2023 |
| Last update date |
Dec 13, 2023 |
| Contact name |
Laila M Poisson |
| E-mail(s) |
lpoisso1@hfhs.org
|
| Organization name |
Henry Ford Health
|
| Street address |
2799 W Grand Blvd
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48202 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE248471 |
The epigenetic evolution of glioma is determined by the IDH1 mutation status and treatment regimen |
|
