Getting TCGA Glioblastoma data through cBioportal
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One really good way to get TCGA glioblastoma data or any TCGA data for that matter, is through cBioportal. In the case of glioblastoma, there is data on 580 patients, published in Cell in 2013. The cBioportal site gives a good breakup of the kinds of data available, as well as excellent visualization tools for preliminary analysis.
Of the 580 patients, there is RNASeq data for 154 of them. The RNASeq expression data has been cleaned and presented as single values per gene, so it is ready to use in an Excel or MS Access format. The data downloads as a compressed tar file which when uncompressed, is a folder of .txt files totaling about 250 MB total size and can be opened on the Path4 server in order to convert the .txt files into Excel files (through OfficeLibre) relatively quickly.
In order to obtain the associated raw, unprocessed data, one can got to the NCI Genomic Data Commons (GDC) website and find it through matching the patient IDs. Although the raw expression values are openly accessible via GDC, access to the raw sequence reads is controlled and perhaps might be unlocked for us if we were to get a special permit as an educational institution.
Of the 580 patients, there is RNASeq data for 154 of them. The RNASeq expression data has been cleaned and presented as single values per gene, so it is ready to use in an Excel or MS Access format. The data downloads as a compressed tar file which when uncompressed, is a folder of .txt files totaling about 250 MB total size and can be opened on the Path4 server in order to convert the .txt files into Excel files (through OfficeLibre) relatively quickly.
In order to obtain the associated raw, unprocessed data, one can got to the NCI Genomic Data Commons (GDC) website and find it through matching the patient IDs. Although the raw expression values are openly accessible via GDC, access to the raw sequence reads is controlled and perhaps might be unlocked for us if we were to get a special permit as an educational institution.