|
| Status |
Public on Mar 28, 2012 |
| Title |
High-grade osteosarcoma pre-chemotherapy biopsy L3538int |
| Sample type |
RNA |
| |
|
| Source name |
High-grade osteosarcoma pre-chemotherapy biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
type: biopsy
gender: unknown
age: unknown
histological subtype: unknown
tumor location: unknown
huvos grade: unknown
matching copy number data: no
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation, cDNA synthesis, cRNA amplification, Illumina Human-6 v2.0 Expression BeadChip hybridization, qPCR validation, and microarray data analysis were performed as previously described (Buddingh EP, Kuijjer ML, Duim RA, Burger H, Agelopoulos K, Myklebost O, et al. Tumor-infiltrating macrophages are associated with metastasis suppression in high-grade osteosarcoma: a rationale for treatment with macrophage-activating agents. Clin Cancer Res 2011 Apr 15;17(8):2110-2119).
|
| 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. Two supplementary/raw data 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).
|
| 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. Poor quality arrays were removed from further analyses.
|
| |
|
| Submission date |
Nov 01, 2011 |
| Last update date |
Mar 29, 2012 |
| 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 (3) |
| GSE33382 |
Genome-wide gene expression analysis of high-grade osteosarcoma |
| GSE33383 |
Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data |
| GSE42352 |
Genome-wide gene expression profiling of mesenchymal stem cells, osteosarcoma cells, and osteosarcoma cell lines. |
|
