Ivy Glioblastoma Atlas project
This is the online help for the Ivy Glioblastoma Atlas Project web application.
The Ivy Glioblastoma Atlas Project is a foundational resource for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels.
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: Initial screen of 8 tumors with 341 probes to glioblastoma-enriched genes.
Anatomic Structures ISH for Enriched Genes: Final screen of 29 tumors with 50 probes to genes enriched in particular anatomic structures as identified in Anatomic Structures RNA-Seq study.
Cancer Stem Cells ISH Survey: Initial screen of 16 tumors with 63 probes to putative cancer stem cell-enriched genes to identify a 20 probe reference set, which was then used in an extensive screen of 41 tumors.
Cancer Stem Cells ISH for Enriched Genes: Final screen of 37 tumors with 79 probes to genes enriched in putative cancer stem cell clusters as identified in Cancer Stem Cells RNA-Seq study.
RNA-Seq: RNA sequencing data for anatomic structures 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 in 9 tumors for a total of 124 RNA samples.
Cancer Stem Cells RNA-Seq: Screen of 75 putative cancer stem cell clusters identified by ISH with 20 probe reference set in 34 tumors for a total of 160 RNA samples.
Specimens: De-identified clinical data for each patient and tumor, and search portal for each tumor block’s ISH and annotated H&E image data. For detailed clinical and sequence data requiring user registration to gain access, see Ivy GAP Clinical and Genomic Database
Ivy GAP Clinical and Genomic Database: Partner database with additional clinical, genomic, and transcriptomic data for Ivy GAP.
The Cancer Genome Atlas (TCGA): NIH-funded initiative for genomic mapping of cancers, including glioblastoma.
Moved from Documentation
The 6 studies generated several data modalities, which are listed below.
• De-identified clinical data for 41 patients including age, gender, initial KPS, neurosurgery (resection number), hemisphere, chemotherapy, radiation therapy, recurrence by 6 months, and multifocality
• MRI anonymized scans (42)
• Resected tumor images (42) with tissue block subdivisions and orientation of tumor in brain
• ISH (22,000) acquired with 20x objective for 0.50μm/pixel resolution of 15K x 18K pixel images
• H&E (11,500) acquired with 20x objective for 0.50μm/pixel resolution of 15K x 18K pixel images
• Annotated anatomic structures in H&E images (11,500)
• Nuclear counts for anatomic structures in H&E images (11,500 data sets)
• RNA-Seq (270 laser microdissection samples) with depth of 15 million mapped reads
• RNA-Seq (27 bulk tumor samples) with 100-150 million mapped reads
• Affymetrix SNP array 6.0
• Fusion genes
• Mutations: EGFR amplification, EGFRvIII deletion, PTEN deletion, IDH1 point mutation
• MGMT methylation status
Tumor derived cell lines and xenografts