|
| Status |
Public on Nov 19, 2024 |
| Title |
UCSF IDH-wildtype glioblastoma 107 initial |
| Sample type |
genomic |
| |
|
| Source name |
Primary human tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary human tumor tissue
patient id: 107
tumor category: initial
|
| Treatment protocol |
Primary human tumor tissue was used as the source of genomic DNA for all patients. 99 tumors were from the initial diagnostic surgical procedure prior to any radiation or chemotherapy treatment, and 127 tumors were from a subsequent surgery for recurrence/progressive disease usually following radiation and/or chemotherapy.
|
| Growth protocol |
Primary human tumor tissue was used as the source of genomic DNA for all patients. No ex vivo culture or xenografting was performed.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using disposable biopsy punches. Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k version 1.0 Human DNA Methylation Beadchips using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting
|
| Description |
IDH-wildtype glioblastoma tumor
205854150104_R08C01
|
| Data processing |
Methylation data were preprocessed using the minfi package (v.1.40.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.
Normalized DNA methylation beta-values and detection p-values
|
| |
|
| Submission date |
Oct 08, 2024 |
| Last update date |
Nov 19, 2024 |
| Contact name |
David A. Solomon |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, San Francisco
|
| Department |
Pathology
|
| Street address |
513 Parnassus Ave, HSW 451
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE279073 |
Longitudinal epigenome analysis of IDH-wildtype glioblastomas from initial and recurrent surgical specimens |
|
