|
| Status |
Public on Feb 24, 2012 |
| Title |
07_38868 |
| Sample type |
RNA |
| |
|
| Source name |
FFPE block, diffuse astrocytic glioma
|
| Organism |
Homo sapiens |
| Characteristics |
tumor type: diffuse astrocytic glioma
who grade: III
subclass: EPL
idh mut status: mut
pten methylation: M
cdkn2a methylation: M
tp53 seq: wt
pten del: Yes
pdgfra ihc: +
p53 ihc: -
p-pras40 ihc: +
egfr amp: No
|
| Growth protocol |
Formalin-fixed parrafin-embedded tissue blocks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were extracted using the miRNEASY FFPE kit from Qiagen and quality was assessed by RPL13a RT-PCR
|
| Label |
biotin
|
| Label protocol |
Following Illumina standard protocol, 300ng RNA were converted to cDNA through reverse transcription reaction with biotinylated primers. The biotinylated cDNA is then annealed to assay oligonucleotides (oligos), and bound to streptavidin conjugated paramagnetic particles (SA‐PMPs)
|
| |
|
| Hybridization protocol |
After the oligo hybridization, mis‐hybridized and non‐hybridized oligos are washed away. The hybridized oligos are then extended and ligated. These products form a synthetic template that is transferred to a PCR reaction containing a fluorescently labeled primer
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
FFPE material/DASL processed
|
| Data processing |
The data were analyzed with GenomeStudio using Illumina default analysis settings. Gene level data was obtained by average the probe level data for each gene. The data were then quantile normalized in Partek
|
| |
|
| Submission date |
Jan 19, 2012 |
| Last update date |
Feb 24, 2012 |
| Contact name |
Jason Huse |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial Sloan-Kettering Cancer Center
|
| Street address |
408 E 69th St. (Z701)
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL14951 |
| Series (1) |
| GSE35158 |
Expression profiling of lower-grade diffuse astrocytic glioma |
|
