Six studies were designed to identify the molecular signatures and measure heterogeneity. In Situ Hybridization (ISH) was used to screen for gene expression enriched in particular structures and cell clusters, and laser microdissection followed by RNA sequencing were used to generate the transcriptomes and identify the genetic markers.
Anatomic Structures ISH Survey
Initial screen of 8 tumors and 343 glioblastoma-enriched genes.
Anatomic Structures RNA-Seq
Screen of 5 structures (Leading Edge, Infiltrating Tumor, Cellular Tumor, Microvascular Proliferation, and Pseudopalisading Cells Around Necrosis) identified by H&E staining in 10 tumors for a total of 122 RNA samples.
Anatomic Structures ISH for Enriched Genes
Final screen of 29 tumors and 37 genes enriched in glioblastoma structures identified in Anatomic Structures RNA-Seq Study.
Cancer Stem Cells ISH Survey
Initial screen of 16 tumors and 55 putative cancer stem cell-enriched genes resulting in a 20 probe reference set, which was then used in an extensive screen of 42 tumors.
Cancer Stem Cells RNA-Seq
Screen of 35 clusters of putative cancer stem cells identified by ISH with a 17 reference probe subset (validated in the Cancer Stem Cells ISH Survey) in 34 tumors for a total of 148 RNA samples.
Cancer Stem Cells ISH for Enriched Genes
Final screen of 37 tumors and 76 genes enriched in clusters of putative cancer stem cells identified in Cancer Stem Cells RNA-Seq Study.
Overall, the dataset spans 42 individual tumors. Each tumor was sub-divided into sub-blocks for processing in one of the six studies. See whitepapers for more details about the tumor specimens, tissue and informatics processing.