|
| Status |
Public on Jun 13, 2017 |
| Title |
MB_SubtypeStudy_55023_methylation |
| Sample type |
genomic |
| |
|
| Source name |
Fresh frozen
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: medulloblastoma
type: primary tumor
subgroup: Group3
subtype_formatted: Group3_alpha
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Snap frozen tissue was digested overnight at 55 C with Proteinase K and SDS in TE. DNA was extracted from the digest with phenol-chloroform and precipitated with ammonium acetate and ethanol. The pellet was resuspended in TE buffer. Bisulfite conversion was carried out according to the manufacturer's instructions for the Zymo EZ DNA Methylation Kit
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Protocol
|
| Scan protocol |
Samples were processed as per manufacturer’s instructions. Raw data files (.idat) generated by the Illumina iScan array scanner
|
| Data processing |
Raw data was processed in R using the minfi (v1.6.0) and IlluminaHumanMethylation450kmanifest (v0.4.0) R Bioconductor packages. We checked all samples for unexpected genotype matches by pairwise correlation of the 65 genotyping probes on the 450k arrays, allowing us to remove remaining duplicates. We ran the detectionP function from the minfi package to identify probes and samples with low quality. Samples were removed if more than 1% of their probes had a p-value above 0.01 and probes were removed if their p-value was above 0.01 in at least 5% of samples. We removed probes on sex chromosomes as well as those located on or close to known single nucleotide polymorphisms (SNP). We retained a total of 321,174 probes for the analysis. The data was normalized using the SWAN method (Makismovic et al., Genome Biology 2012) as implemented in the minfi package. The matrix of normalized beta values is available on the series record.
|
| |
|
| Submission date |
Aug 04, 2016 |
| Last update date |
Jun 11, 2019 |
| Contact name |
Florence M G Cavalli |
| E-mail(s) |
fmgcavalli@gmail.com
|
| Organization name |
The Hospital for Sick Children
|
| Department |
Developmental and Stem Cell
|
| Street address |
PGCRL, 686 Bay Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE85212 |
DNA methylation profiling of primary medulloblastoma samples |
| GSE85218 |
DNA methylation and gene expression profiling of primary medulloblastoma samples |
|
| Relations |
| Reanalyzed by |
GSM3876847 |
