|
| Status |
Public on Nov 01, 2014 |
| Title |
CPC, CP6-T |
| Sample type |
genomic |
| |
|
| Source name |
choroid plexus tumor, CPC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: choroid plexus tumor
subgroup: choroid plexus carcinoma
p53 status: mut
tissue type: FFPE
|
| Treatment protocol |
DNA was isolated from fresh-frozen samples (snapped frozen in liquid nitrogen) (n=17) and an optimal cutting temperature compound (OCT)-embedded fresh frozen sample (n=1), and formalin-fixed paraffin-embedded (FFPE) samples (n=2).
|
| Growth protocol |
n/a
|
| 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 (Ambion, Carlsbad, USA) for FFPE samples.
|
| Label |
n/a
|
| Label protocol |
n/a
|
| |
|
| Hybridization protocol |
20 tumor DNA samples were hybridized to Affymetrix OncoScan™ FFPE Express 2.0 arrays at St. Jude Children's Research Hospital.
|
| Scan protocol |
Standard Affymetrix protocol.
|
| Description |
CP6-T
Brain tumor
|
| Data processing |
Undertaken using the SNP-FASST2 Segmentation Algorithm within Nexus Copy number software (Discovery Edition 7.0, BioDiscovery, Hawthorne, CA) and NCBI genome build 37.
*probes.txt: Log2 ratio per probe generated by Nexus Copy Number Software.
|
| |
|
| Submission date |
Sep 11, 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 |
GPL15793 |
| Series (2) |
| GSE60886 |
Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups |
| GSE61363 |
Genome-wide copy number and allele-specific copy number analysis of choroid plexus tumors (II) |
|
