|
| Status |
Public on Nov 01, 2014 |
| Title |
CP107-TA |
| Sample type |
RNA |
| |
|
| Source name |
brain tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: choroid plexus papillomas
p53 status: mut
|
| Treatment protocol |
Fresh-frozen samples (snapped frozen in liquid nitrogen).
|
| Growth protocol |
Total RNA was isolated from fresh-frozen tumor soon after tumor resection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIzol method (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
not provided
|
| |
|
| Hybridization protocol |
Hybridization of total RNA to GeneChip® Human Exon 1.0ST gene expression 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 |
cpp
|
| Data processing |
Gene expression analysis was conducted in Partek GS6.5 with the following uploading parameters: Probes to import: Interrogating Probes and Control Probes. Probe filtering: Include Core Meta-Probeset: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps. Pre-background Adjustment: Adjust for GC Content. Background correction: RMA Background correction. Normalization: one-way anova normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish. ANOVA statistical test was used to identify gene expression differences between subgroups.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| 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 |
GPL5175 |
| Series (2) |
| GSE60886 |
Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups |
| GSE60892 |
Gene expression analysis of choroid plexus tumors |
|
