|
| Status |
Public on Jan 10, 2022 |
| Title |
UCSF Meningioma 119 (methylation) |
| Sample type |
genomic |
| |
|
| Source name |
Meningioma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: meningioma
institution: UCSF
age: 42.9
Sex: 2
grade: 2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Meningiomas were removed, flash frozen in liquid nitrogen, mechanically lysed using a TissueLyser II, and DNA was extracted from the lysed tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (CAT# 80224)
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
meningioma
M119
202225190152_R08C01
|
| Data processing |
Analysis was performed in R v3.5.3 with the SeSAMe package. Probes were filtered and analyzed using the standard SeSAMe preprocessing pipeline, including normal-exponential out-of-band background correction, nonlinear dye bias correction, p-value with out-of-band array hybridization masking, and beta value calculation
Processed data file meningioma_betas.csv represents SeSAMe-computed average beta values.
|
| |
|
| Submission date |
Sep 07, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Abrar Choudhury |
| Organization name |
University of California, San Francisco
|
| Street address |
1450 3rd St
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE183647 |
Meningioma DNA methylation grouping reveals biologic drivers and therapeutic vulnerabilities (array) |
| GSE183656 |
Meningioma DNA methylation grouping reveals biologic drivers and therapeutic vulnerabilities |
|
