|
| Status |
Public on Nov 01, 2014 |
| Title |
CP4-T |
| Sample type |
genomic |
| |
|
| Source name |
brain tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: atypical choroid plexus papillomas
p53 status: wt
tissue source: DNA
|
| Treatment protocol |
DNA was isolated from fresh-frozen samples (snapped frozen in liquid nitrogen) (n=46) and optimal cutting temperature compound (OCT)-embedded fresh frozen (n=8), and formalin-fixed paraffin embedded (FFPE) (1) samples.
|
| Growth protocol |
DNA was isolated from fresh-frozen tumor soon after tumor resection
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor genomic DNA was extracted using standard phenol-chloroform extraction from fresh-frozen samples, and the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Ambion, Carlsbad, USA) from FFPE samples.
|
| Label |
biotin
|
| Label protocol |
not provided
|
| |
|
| Hybridization protocol |
Hybridization of genomic DNA to Genome-Wide Human SNP Array 6.0 genotyping microarrays took place at the Toronto Centre of Applied Genomics (TCAG) at the Hospital for Sick Children in Toronto, Canada, according to manufacturer's instructions.
|
| Scan protocol |
not provided
|
| Description |
acpp
|
| Data processing |
Partek® Genomics Suite™ 6.5 (PGS) (Partek Inc. St. Louis, USA) was used for initial copy number analysis. Inferred copy number states (regions of deletion or duplication) were derived from Partek's genomic segmentation algorithm (Partek, St Louis,MO) such that segmented regions were significantly different from neighbouring regions (p<0.001) and contained 10 or more probes, with a signal to noise ratio of 0.3. Diploid samples were those with a copy number between 1.75-2.25. Segmentation assumed all somatic chromosomes were diploid. Annotation file: GenomeWideSNP_6.na33.annot.csv
Copy number (by Genomic Segmentation algorithm) and allele ratio data provided.
|
| |
|
| Submission date |
Aug 28, 2014 |
| Last update date |
Nov 01, 2014 |
| Contact name |
Diana M Merino |
| E-mail(s) |
diana.merino@utoronto.ca
|
| Organization name |
The Hospital for Sick Children
|
| Department |
Genetics and Genome Biology
|
| Lab |
Malkin
|
| Street address |
686 Bay St.
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5V0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE60886 |
Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups |
| GSE60899 |
Genome-wide copy number and allele-specific copy number analysis of choroid plexus tumors (I) |
|
