Research
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
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* Corresponding author: Sampsa Hautaniemi sampsa.hautaniemi@helsinki.fi
- † Equal contributors
1 Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Haartmaninkatu 8, Helsinki, FIN-00014, Finland
2 Medical Biotechnology, VTT Technical Research Centre and University of Turku, Itäinen Pitkäkatu 4C, Turku, FI-20521, Finland
3 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, FI-20520, Finland
4 Department of Pathology, University of Turku and Turku University Hospital, Kiinamyllynkatu 4-8, Turku, FI-20521, Finland
Genome Medicine 2010, 2:65 doi:10.1186/gm186
Published: 7 September 2010Additional files
Additional file 1:
Automatically generated result file. The report contains analysis configurations, parameter settings, result lists, tables and figures. The document also includes some analyses not reported in the manuscript, such as Gene Ontology analysis.
Format: ZIP Size: 11.8MB Download file
Additional file 2:
Information and data for siRNA screens. The information includes identifiers, siRNA target sequences, normalized mean intensities, standard errors of the mean and P-values for four cell lines used.
Format: XLS Size: 114KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 3:
Screenshot from the Anduril-generated web site. Genes are sorted in decreasing order according to the fraction of amplification ('Gain') in the GBM samples. The strongest amplified region in the GBM samples is 7p11.2. Interestingly, the expression values of the genes in the same genomic region vary significantly. For example, EGFR is amplified and has high fold change whereas LANCL2 is amplified and downregulated (panel A). The same phenomenon is seen in another amplified region 12q14.1 (panel B).
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Additional file 4:
Screenshot from the Anduril-generated web site. Genes are sorted in decreasing order according to the fraction of deletion ('Loss') in the GBM samples. The strongest deleted region in the GBM samples is 9p21.3. The fraction of deletion varies from 35% to 69%.
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Additional file 5:
The effect of gene silencing on cell proliferation. Control siRNAs (13 nM final concentration) were transfected with Silenfect (BioRad) transfection reagent to A172, LN405 and U87MG glioma cell lines and the SVGp12 control cell line. Cell proliferation was assayed 72 h after transfection using CellTiter-Glo Cell Viability assay. The proliferation data are presented as relative score to the mean of scramble siRNA-containing wells. Error bars indicate median absolute deviation.
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Additional file 6:
The effect of gene silencing on caspase-3 and -7 activities. Control siRNAs (13 nM final concentration) were transfected with Silenfect (BioRad) transfection reagent to A172, LN405 and U87MG glioma cell lines and the SVGp12 control cell line. Induction of caspase-3 and -7 activities was detected 48 h after transfection with homogeneous Caspase-Glo 3/7 assay (Promega). The caspase activity is presented as relative median score to the mean of scramble siRNA containing wells. Error bars indicate median absolute deviation.
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Additional file 7:
The effects of silencing CDKN2A in LN405 and SVGp12 cell lines on cell proliferation and apoptosis.
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