|
| Status |
Public on Aug 30, 2012 |
| Title |
8530 SMZL methylation |
| Sample type |
genomic |
| |
|
| Source name |
8530 SMZL methylation
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Splenic marginal zone lymphoma
|
| Treatment protocol |
2μg genomic DNA extracted from frozen tissues with >70% tumour cells using Qiagen kit
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA extracted from frozen tissues was bisulphite modified using the EZ DNA Methylation Kit (Zymo Research Corporation)
|
| Label |
Cy3, Cy5
|
| Label protocol |
Bisulphite modified DNA was then amplified using the MSM master mix (Illumina) and incubated at 37oC for 22 hours. Amplified DNA was then fragmented and hybridised to BeadChips in an Illumina Hybridisation Oven at 48oC for 18 hours
|
| |
|
| Hybridization protocol |
Following hybridisation, single base extension of hybridised DNA using hapten labelled bases was performed. Staining was then developed using immunochemical stains catalysed by the haptens, and the arrays washed
|
| Scan protocol |
The chips were scanned using the BeadArray™ Reader (Illumina) and the BeadScan™ software (Illumina) using the Infinium Methylation Scan setting. The scanned data was then analysed in GenomeStudio™ (Illumina) using the Methylation analysis module
|
| Data processing |
The scanned data bead file was spatially normalised to correct for background noise using the Smethillium algorithm (http://bioinfo-out.curie.fr/projects/smethillium) within the R environment (www.r-project.org). Where multiple probes targeted different CpG loci relating to one gene, the probe predicted to have the greatest influence on gene expression (eg. at a transcriptional factor binding site, proximity to the promoters) was selected for analysis
|
| |
|
| Submission date |
Jan 30, 2012 |
| Last update date |
Aug 30, 2012 |
| Contact name |
Alan J Watkins |
| E-mail(s) |
a.j.watkins@doctors.org.uk
|
| Organization name |
University of Cambridge
|
| Street address |
Addenbrooke's Hospital
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE21554 |
An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Main Study) |
| GSE35424 |
An integrated genomic and expression analysis of 7q deletion in SMZL (Illumina Infinium Human Methylation 27 array) |
|
