|
| Status |
Public on Jan 22, 2013 |
| Title |
OS_Biopsy_9 (mRNA) |
| Sample type |
RNA |
| |
|
| Source name |
Osteosarcoma biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
age: 11 years
gender: male
chemotherapy: MAP 2 pre-surgery, 3 post
percent necrosis: >90% necrosis
recurrence: Y
death: N
time until first recurrence or latest follow-up (months): 19.5
tissue: osteosarcoma
biopsy/resection pair: NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from FFPE blocks using the Qiagen RNeasy kit according to company protocol.
|
| Label |
biotin
|
| Label protocol |
Total RNA underwent a reverse transcription reaction to generate double-stranded cDNA. Standard Illumina protocols followed (Whole-Genome DASL HT Assay Kits #'s DA-905-0024, DA-905-0096, DA-905-1024, DA-905-1096).
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol. Arrays were washed and stained with strepatavidin-Cy3, and then scanned in the array reader.
|
| Scan protocol |
Standard Illumina scanning protocol using the Illumina BeadArray Reader.
|
| Data processing |
Expression data were imported to the R environment and processed using the Illumina-specific package lumi. Variance-stabilizing transformation (VST) and quantile normalization were applied. VST is described in Lin SM, Du P, Huber W, Kibbe WA. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 2008 36:e11 (PMID 18178591).
|
| |
|
| Submission date |
Jul 02, 2012 |
| Last update date |
Jan 22, 2013 |
| Contact name |
Katherine Hill |
| E-mail(s) |
[email protected]
|
| Organization name |
Beth Israel Deaconess Medical Center
|
| Department |
Medicine
|
| Lab |
Dimitrios Spentzos
|
| Street address |
330 Brookline Avenue, DA-679
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL14951 |
| Series (2) |
| GSE39055 |
mRNA profiling and clinical outcomes in human osteosarcoma (biopsies) |
| GSE39058 |
microRNA- and mRNA-based studies in paraffin-archived human osteosarcoma specimens reveal profiles with reproducible and independent prognostic value |
|
