|
Status |
Public on Nov 01, 2014 |
Title |
aCPP, CP159-T |
Sample type |
genomic |
|
|
Source name |
choroid plexus tumor, aCPP
|
Organism |
Homo sapiens |
Characteristics |
tissue: choroid plexus tumor subgroup: atypical choroid plexus papilloma p53 status: wt tissue type: frozen
|
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 |
CP159-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) |
|