|
| Status |
Public on Jun 11, 2019 |
| Title |
7973219008_R05C02 |
| Sample type |
genomic |
| |
|
| Source name |
medulloblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cohort: GSE85212
tissue: Medulloblastoma
subgroup: MB_G4
subtype: 8
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and purified from medulloblastoma samples using standard extraction protocols.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina protocol.
|
| |
|
| Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and Infinium MethylationEPIC Beadchips using standard Illumina protocol.
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.
|
| Data processing |
Arrays were imported and quality control performed using minfi.
Beta values - A correction for the type of material (FFPE/frozen) was performed by using the removeBatchEffect function of the limma package v.3.24.15. The log2-transformed intensities of the methylated and unmethylated signal were corrected individually. Beta-values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina) and used for all downstream analyses.
GSE130051_beta_values.csv: Beta values; Rows are Samples, columns are ID_REFs.
GSE130051_transposed_beta_values.csv: Beta values; Rows are ID_REFs, columns are Samples.
|
| |
|
| Submission date |
Jun 11, 2019 |
| Last update date |
Jun 20, 2019 |
| Contact name |
Ed Schwalbe |
| E-mail(s) |
ed.schwalbe@northumbria.ac.uk
|
| Organization name |
Northumbria University
|
| Department |
Applied Sciences
|
| Street address |
Ellison Place
|
| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE1 8ST |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE130051 |
Second-generation molecular subgrouping of medulloblastoma: an international meta-analysis of Group 3 and Group 4 subtypes |
|
| Relations |
| Reanalysis of |
GSM2261161 |
