Data Types

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.
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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

Access Raw Genomics Data
Data Types