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Ivy Glioblastoma Atlas Project

The Ivy Glioblastoma Atlas Project is a foundational resource for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels.

Partnership

The Ivy Glioblastoma Atlas Project is a collaborative partnership between the Ben and Catherine Ivy Foundation, the Allen Institute for Brain Science, and the Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment.

Funding Support

This project was supported by the Ben and Catherine Ivy Foundation (PIs: Ralph Puchalski, PhD, Allen Institute for Brain Science and Greg Foltz, MD, Swedish Neuroscience Institute). The content is solely the responsibility of the respective authors and does not necessarily represent the official views of the Ben and Catherine Ivy Foundation.

CONTRIBUTORS
The Ben & Catherine Ivy Foundation
Allen Institute for Brain Science website
The Ben and Catherine Ivy Center for Advanced Brain Tumor

Data Overview

The Ivy Glioblastoma Atlas Project includes the following data sets

  • ISH: Image data at cellular resolution of in situ hybridization (ISH) tissue sections and adjacent hematoxylin and eosin (H&E)-stained sections annotated for anatomic structures
    • Anatomic Structures ISH Survey: Primary screen of 8 tumors with probes for 343 genes enriched in glioblastoma.
    • Anatomic Structures ISH for Enriched Genes: Subsequent screen of 29 tumors with probes for 37 genes enriched in glioblastoma structures identified in Anatomic Structures RNA-Seq Study (see below).
    • Cancer Stem Cells ISH Survey: Primary screen of 16 tumors with probes for 55 genes enriched in putative cancer stem cells, resulting in a 20 probe reference set, which was then used in an extensive screen of 42 tumors.
    • Cancer Stem Cells ISH for Enriched Genes: Subsequent screen of 37 tumors with probes for 76 genes enriched in clusters of putative cancer stem cells identified in the Cancer Stem Cells RNA-Seq Study (see below).

  • RNA-Seq: RNA sequencing data for anatomic structures identified in the Anatomic Structures ISH Survey and putative cancer stem cell clusters isolated by laser microdissection
    • 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. A total of 122 RNA samples were generated from 10 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). A total of 148 RNA samples were generated from 34 tumors.

  • Specimen Metadata: De-identified clinical data for each patient and tumor.

  • Related Resources