|
| Status |
Public on Oct 27, 2012 |
| Title |
human sporadic medulloblastoma tumor_HMED13 |
| Sample type |
RNA |
| |
|
| Source name |
human medulloblastoma tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age (yr): 8
tumor grade (histological): IV
molecular subgroup: SHH
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tumor tissues using the mirVANA kit ( Ambion, Austin, TX, USA) , as per the manufacturer’s protocol after ensuring at least 80% tumor cell content.The RNA was further purified using RNeasy columns (Qiagen,Valencia, CA, USA), for removing genomic DNA contamination if at all . RNAs having more than 7.0 RIN value and no detectable genomic DNA contamination were used for the analysis.
|
| Label |
biotin
|
| Label protocol |
100 ng total RNA was reverse transcribed, amplified, and labeled with biotin using the whole transcript sense target labeling kit as per the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).
|
| |
|
| Hybridization protocol |
Following fragmentation, 2 ug cRNA was hybridized for 16 hr at 45°C on Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip scanner 2500.
|
| Description |
Gene expression data of human medulloblastoma tumor tissue
|
| Data processing |
Data normalization was done using GCRMA algorithm in the Bioconductor package (v 2.1) of the R statistical environment (http://www.bioconductor.org)
|
| |
|
| Submission date |
Oct 26, 2012 |
| Last update date |
Jan 08, 2019 |
| Contact name |
Neelam V Shirsat |
| E-mail(s) |
nshirsat@actrec.gov.in
|
| Organization name |
Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre
|
| Department |
Shirsat Lab
|
| Street address |
Kharghar, Sector 21
|
| City |
Navi Mumbai |
| State/province |
Maharashtra |
| ZIP/Postal code |
410210 |
| Country |
India |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE41842 |
Distinctive microRNA signature of medulloblastomas associated with the WNT signaling pathway |
|
| Relations |
| Reanalyzed by |
GSE124814 |
