|
| Status |
Public on Jun 22, 2023 |
| Title |
Patient4 meningioma |
| Sample type |
genomic |
| |
|
| Source name |
meningioma
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: FEMALE
age: 60
who grade: I
reoperation: Yes
progression: Yes
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor/dura samples were obtained at the time of surgery. DNA was extracted using Qiagen DNeasy Blood & Tissue Kit (Cat No./ID: 69506).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Purified DNA underwent bisulfite conversion using Zymo EZ DNA Methylation kit (Cat No.: D5001) then labeled using standard Illumina protocol.
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
meningioma
4M
|
| Data processing |
Copy number variant detection: Raw IDAT files were imported with the R Bioconductor package minfi and the preprocessIllumina normalization function was used to generate a GenomicRatioSet object for input into conumee. The 12 dura samples were used as controls. To generate ratios for meningioma-specific detail lists, the list of oncogenes included with the conumee package was appended to include genes previously identified as mutated in meningiomas, components of the BAF (SWI/SNF) complex, and chromosomal regions that have been associated with aggressive behavior in meningiomas. A ratio cutoff of +/-0.25 to call amplifications (>0.25) or deletions (<0.25). Additionally, tumor/dura ratios generated for the loci included in the detail list were used with a cutoff of +/-0.25 to call loci as amplified (>+0.25), neutral (-0.25 to +0.25), or deleted (<-0.25) using custom scripts written in R. Methylation Analysis: Raw red/green IDAT files were imported into R using the package minfi to obtain beta-values and M-values after functional normalization. Mapping to the hg38 genome build and general masking filtering criteria of Zhou et al., Nucleic Acids Research 2017 were used for all downstream analysis. To determine the fraction of methylated probes in the promoter region of each gene, probes mapping within +/-2kb of transcription start sites (TSS) of all genes in the the GENCODE v29 primary assembly were identified. and called as methylated or hemi-methylated (β value >=0.3) or unmethylated (β value <0.3). The percentage of methylated probes in each promoter region was calculated as (#methylated probes)/(total #probes)*100.
Normalized beta-values (functional normalization)
|
| |
|
| Submission date |
Jun 14, 2021 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Michelle Ariana Wedemeyer |
| E-mail(s) |
michelle.ariana.wedemeyer@gmail.com
|
| Organization name |
University of Southern California
|
| Department |
Neurosurgery
|
| Street address |
1200 N State St, Suite 3300
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE178139 |
DNA Methylation Signatures Differentiate Meningiomas from Normal Dura [HumanMethylation450] |
| GSE178143 |
DNA Methylation Signatures Differentiate Meningiomas from Normal Dura |
|
