The Ivy GAP is described in the resource paper: Puchalski RB, Shah N, …Foltz GD. An anatomic transcriptional atlas of human glioblastoma. Science360, 660-663 (2018). doi:10.1126/science.aaf2666. For
For scientific or other inquiries about this dataset, please contact: Nameeta Shah Ph.D. (email@example.com). please contact the TCIA Helpdesk.
Number of Participants
Number of Studies
Number of Series
Number of Images
|Image Size (GB)||130.4|
In addition to the DICOM images in TCIA there are two additional databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities:
- The Ivy Glioblastoma Atlas Project web site includes the following data:
- 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.
- The Ivy GAP Clinical and Genomic Database contains detailed clinical information including pathology images, genomic data, and prospectively collected outcomes data. This site requires separate registration.
|title||Citations & Data Usage Policy|
Citations & Data Usage Policy
|Public collection license|
Nameeta Shah, Ph.D., Xu Feng, Ph.D., Michael Lankerovich, Ph.D., Ralph B. Puchalski, Ph.D., Bart Keogh, M.D., Ph.D. (2016). Data from Ivy GAP. The Cancer Imaging Archive. http://dx.doi.org/10.7937/K9/TCIA.2016.XLwaN6nL
Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF. An anatomic transcriptional atlas of human glioblastoma. Science. 2018 May 11;360(6389):660-3. DOI: 10.1126/science.aaf2666
Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. (paper)
Other Publications Using This Data
TCIA maintains a list of publications that leverage our data. At this time, we are not aware of any publications based on this data. If you have a publication you'd like to add, please contact the TCIA Helpdesk.
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Version 1 (Current): Updated 2016/12/30
|Data Type||Download all or Query/Filter|
|Images (DICOM, 130.4GB)|
|Summary ISH, RNA, gene expression and clinical data|
|Detailed clinical, genomic, and expression array data|