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Sample GSM322694 Query DataSets for GSM322694
Status Public on Sep 08, 2009
Title 178 replicate 2
Sample type RNA
 
Source name osteosarcoma tumor 178
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 178 bioreplicate 2
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

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
7892501 5.30519
7892502 5.86082
7892503 3.68279
7892504 8.92395
7892505 3.43907
7892506 4.50226
7892507 6.05697
7892508 6.17101
7892509 11.1499
7892510 7.0434
7892511 3.80187
7892512 7.78152
7892513 3.68279
7892514 10.5843
7892515 9.51773
7892516 6.28657
7892517 7.72157
7892518 2.12764
7892519 6.86853
7892520 9.89305

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM322694.CEL.gz 4.0 Mb (ftp)(http) CEL
GSM322694.chp.gz 255.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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