Disease Cohort-Level Data
- Single-cell/Single-nucleus RNA-sequencing data set from patient tumors and associated O-PDX tumors. Samples are annotated based on histologic type, developmental state, and predicted cell cycle phase. Patient tumor datasets contain separate viewers for malignant nuclei (>111,000 nuclei) or non-malignant nuclei (>11,000 nuclei). O-PDX datasets contain a viewer for >100,000 cells
- Epigenetic data includes whole genome bisulfite (WGBS) and ChIP-seq data for eight histone marks and CTCF, Brd4 and RNA PolII for a total of over 750 ChIP-seq libraries. The data have been integrated to define chromatin states using chromatin Hidden Markov Modeling. (Access browsers for neuroblastoma, osteosarcoma, rare tumors, and rhabdomyosarcoma)
- Methylation Classification DNA methylation profiling was performed as part of the solid tumor Comprehensive METhylation (COMET) Blue Sky project, a collection of >4700 samples including patient tumors, Xenografts, and cell lines.
- Somatic mutations for patient tumors compared with O-PDX tumors using Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES).
- Chemical sensitivity for O-PDX tumors in vitro screened against 156 different drugs with filter on mechanism of action, disease type and overlay EC50 curves.
Sample-Level Data
- Sample details including clinical information, assays performed, material available in a characterization sheet (pdf) for individual non-interactive data for each sample
- Genomic data including WGS, WES and RNA-sequencing of O-PDX, patient tumor and germline (only WGS/WES) for each sample
- Clonal analysis determining whether the clonal population in the O-PDX recapitulates the patient tumor (Access clonal evolution example)
- Histology IHC comparing O-PDX with patient tumor (H&E for all, additional disease specific stains)
- Electron microscopy of O-PDX samples in three magnifications: 5000, 19000 and 29000 to visualize internal cell structure and confirm recapitulation
- DNA Profile for short tandem repeat validation to confirm O-PDX models between passages
- Somatic mutations for patient tumors compared with O-PDX tumors using WGS and WES (static sample heatmap and circos plots)
Gene Search
- Interactive feature to create custom heatmaps based on genes and diagnoses
- Explore small variant and structural variant of patient tumor and O-PDX tumors
