|
| Status |
Public on Nov 30, 2014 |
| Title |
VestibularSchwannoma_Sporadic_20 |
| Sample type |
genomic |
| |
|
| Source name |
Vestibular Schwannoma (Sporadic)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Vestibular Schwannoma
tissue type: Tumor
subtype: Sporadical
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the Wizard Genomic DNA purification kit (Promega), according to the manufacturer’s instructions. Bisulfite-treated using the EZ DNA methylation Kit (Zymo Research, Orange, CA, USA), according to the manufacturer’s instructions.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip, using standard Illumina protocols.
|
| Scan protocol |
Arrays were scanned using BeadArray Reader by standard recommended Illumina scanner settings
|
| Data processing |
M-value was obtained with lumi R package after background correction, color bias adjustment by quantiles and SSN normalization
ProcessedMatrix.txt: Avg_Beta correspond to M-value after processing with lumi package: Barckground correction, color bias adjustment and normalization by ssn. p_value were obtained with GenomeStudio. This table is prepared for using in IMA package.
Rawdata.txt: Value outputed by lumi package after direct import from iDAT files. Was done using importMethyIDAT function, which give this non-processed value.
|
| |
|
| Submission date |
Apr 08, 2014 |
| Last update date |
Nov 30, 2014 |
| Contact name |
Miguel Torres-Martin |
| E-mail(s) |
migtorres.martin@gmail.com
|
| Organization name |
Hospital Universitari Germans Trias i Pujol
|
| Department |
Clinical Genomics Unit
|
| Street address |
Carretera de Canyet, s/n
|
| City |
Badalona |
| State/province |
Barcelona |
| ZIP/Postal code |
08916 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE56596 |
Wide methylation analysis in vestibular schwannoma [Infinium HumanMethylation450 BeadChip] |
| GSE56598 |
Wide methylation analysis in vestibular schwannoma |
|
