|
Status |
Public on Dec 13, 2023 |
Title |
glioma_Primary [TCGA-06-0125-TP-01M-450-XC6ZJF] |
Sample type |
genomic |
|
|
Source name |
TCGA-06-0125
|
Organism |
Homo sapiens |
Characteristics |
gender: female age_diagnosis_years: 63 surgical_interval_mo: 0 who.classification.2021: Glioblastoma, IDH-wildtype (WHO grade 4) recurrent_status: Primary idh_status: IDHwt codel_status: noncodel tcga.subtype: Classic-like heidelberg_meth_subtype: RTK II
|
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-06-0125-TP-01M-450-XC6ZJF
|
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
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|
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 |
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