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Sample GSM322700 Query DataSets for GSM322700
Status Public on Sep 08, 2009
Title 182 replicate 2
Sample type RNA
 
Source name osteosarcoma tumor 182
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 182 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) [email protected]
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 6.07034
7892502 5.96215
7892503 5.49586
7892504 10.0532
7892505 3.50243
7892506 5.20803
7892507 7.07949
7892508 7.8029
7892509 10.5907
7892510 7.71172
7892511 4.49349
7892512 8.08893
7892513 3.60867
7892514 9.762
7892515 10.1094
7892516 6.90107
7892517 7.08058
7892518 3.83096
7892519 7.08501
7892520 10.4026

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM322700.CEL.gz 4.0 Mb (ftp)(http) CEL
GSM322700.chp.gz 256.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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