|
| Status |
Public on Sep 08, 2009 |
| Title |
180 replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
osteosarcoma tumor 180
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pediatric osteosarcoma
|
| Treatment protocol |
Cells were harvested with Tripsin (Invitrogen) as per manifacturers instructions
|
| Growth protocol |
Normal human osteoblasts (HOB) are primary osteoblasts from the hip bone of a normal male donor that were purchased from PromoCell (Heidelberg, Germany, Catalogue # C-12760) and maintained in medium provided by the manufacturer and used at culture passage 3. Three days after plating (~80% confluent), cells where harvested for DNA or RNA extractions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from tumours cells and HOB was extracted using the TRIzol reagent method as per manifacturers instructions (Invitrogen, Osaka, Japan).
|
| Label |
TdT labeling kit
|
| Label protocol |
Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).
|
| |
|
| Hybridization protocol |
Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).
|
| Scan protocol |
Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).
|
| Description |
gene expression data 180 bioreplicate 1
|
| Data processing |
Data from RNA expression array experiments in the form of .cel files (GCOS 1.3 software) were imported into and analysed using the Partek Genomic Suite Software (PGS). The expression array .cel files for osteoblasts and tumour samples (2 arrays each) were imported using PGS Gene Expression Workflow tool (subject to RMA normalization and log2 transformation). The significantly over- and under-expressed genes in tumours compared to normal osteoblasts were detected using 1-way ANOVA tool at p<0.01 and +/- 2-fold enrichment, either specifically for each tumour sample or cumulatively (i.e. mean signal of all tumours vs. osteoblasts). Significantly over- and under-expressed regions were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the HuGene-1_0-st-v1.na24.hg18.transcript.csv file.
|
| |
|
| Submission date |
Sep 19, 2008 |
| Last update date |
Aug 10, 2012 |
| Contact name |
Bekim Sadikovic |
| E-mail(s) |
bsadikov@gmail.com
|
| Organization name |
The SickKids Hospital and Princess Margaret Hospital
|
| Street address |
555 University Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1X8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE12865 |
Gene expression of human paediatric osteosarcoma tumour samples relative to normal human osteoblasts |
| GSE12885 |
Genome-wide changes in DNA methylation and copy number play a role in deregulation of gene expression in osteosarcoma |
|
