|
| Status |
Public on Feb 11, 2011 |
| Title |
19264-05 |
| Sample type |
RNA |
| |
|
| Source name |
Osteosarcoma pre-chemotherapy biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
age: 181 months
gender: M
histological subtype: Sclerosing
tumor location: Right proximal tibia
huvos grade: 1
group: Metastases at 25 months after diagnosis of the primary tumor
status: Alive at 25 months after diagnosis of the primary tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Osteosarcoma tissue was snap-frozen in 2-Methylbutane (Sigma-Aldrich, Zwijndrecht, the Netherlands) and stored at -70°C. Using a cryostat, 20 µm sections from each block were cut and stained with hematoxylin and eosin to ensure at least 70% tumor content and viability. RNA was isolated using TRIzol reagent (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit (Venlo, the Netherlands) with on-column DNAse treatment, according to manufacturers instructions. RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA) and Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.
|
| Label |
biotin
|
| Label protocol |
As per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
As per manufacturer's instructions.
|
| Scan protocol |
As per manufacturer's instructions.
|
| Description |
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format.
|
| Data processing |
Data were analyzed using the statistical language R. As Illumina identifiers are not stable and consistent between different chip versions, raw oligonucleotide sequences were converted to nuIDs. Data were transformed using the variance stabilizing transformation (vst) algorithm and subsequently normalized using robust spline normalization. Conversion to nuIDs, variance stabilizing transformation, and normalization of the data were all carried out using the Bioconductor package lumi. Quality control was performed using the Bioconductor package arrayQualityMetrics. Two supplementary/raw files are present, because each array that represents one sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).
|
| |
|
| Submission date |
Apr 08, 2010 |
| Last update date |
Feb 12, 2011 |
| Contact name |
Marieke Lydia Kuijjer |
| Organization name |
Centre for Molecular Medicine Norway
|
| Lab |
Kuijjer
|
| Street address |
Gaustadalléen 21
|
| City |
Oslo |
| ZIP/Postal code |
0349 |
| Country |
Norway |
| |
|
| Platform ID |
GPL10295 |
| Series (1) |
| GSE21257 |
Genome-wide gene expression profiling on pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5yrs (n=34) and patients who did not develop metastases within 5yrs (n=19) |
|
