|
| Status |
Public on Dec 21, 2022 |
| Title |
HR26 (array) |
| Sample type |
genomic |
| |
|
| Source name |
FFPE brain tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma
tissue: Brain
tumor stage: tumor
ffpe (yes/no): yes
age (yr): 11
Sex: male
treatment: non-treated
tumor grade: low-grade
risk (low/intermediate/high): high
outcome: metastatic
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared following the instructions of a QIAamp DNA FFPE Tissue Kit.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Protocol
|
| Scan protocol |
Standard Illumina Protocol
|
| Description |
204972790059_R01C01
|
| Data processing |
Raw signal intensities from IDAT files were normalized using the functional normalization method implemented in minfi (v.1.38.0). Poor quality (P > 0.01) and failed probes were removed from the downstream analysis. The probes targeting the X and Y chromosomes, containing single-nucleotide polymorphism, and not mapping uniquely to the human reference genome (hg19) were also filtered out.
Identification of differentially methylated probes and regions were performed using limma (v3.48.0) and bumphunter.
Genes within differentially methylated regions were queried against MSigDB v7.4.
|
| |
|
| Submission date |
Mar 24, 2022 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Jason Chiang |
| E-mail(s) |
Jason.Chiang@stjude.org
|
| Phone |
9015951035
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL23976 |
| Series (2) |
| GSE199358 |
The clinical and molecular characteristics of progressive hypothalamic/optic pathway pilocytic astrocytoma [850k array] |
| GSE199362 |
The clinical and molecular characteristics of progressive hypothalamic/optic pathway pilocytic astrocytoma |
|
