Data Files

Overview

The dataset spans four clinical time points and includes whole genome sequencing (WGS), whole exome sequencing (WES), bulk RNA-seq, single-cell RNA-seq (Illumina & Oxford Nanopore), spatial transcriptomics, flow cytometry, and pathology imaging.

Bucket Storage by Directory

Bulk DNA Sequencing

DNA sequencing is available at four time points (T0–T3), including both whole exome (WES) and whole genome (WGS) data.

Whole Genome Sequencing (WGS)

Variant Calling (WGS)

Whole Exome Sequencing (WES)

Bulk RNA Sequencing

Bulk RNA-sequencing is available at three tumor time points (T0, T1, T2), including both short-read (Illumina) and long-read (PacBio) data.

Single Cell RNA-seq (Tumor)

Tumor single-cell and long-read RNA sequencing data from UCSF, spanning time points T1–T3. Includes 10x Illumina scRNA-seq and Oxford Nanopore (ONT) long-read sequencing.

Illumina scRNA-seq (UCSF)

All Illumina scRNA-seq data generated by UCSF

Kamil’s Tumor scRNA-seq Analysis (GEX, TCR, CNV)

Re-analysis of tumor scRNA-seq data by Kamil, including Cell Ranger multi outputs (GEX + TCR + BCR), scanpy-based clustering, cell type prediction, and CNV analysis.

Oxford Nanopore (ONT) Long-Read RNA-seq

All ONT data generated by UCSF

Merged Objects (T1 + T2 + T3)

Longitudinal Single Cell RNA-seq (PBMC)

Sorted live T cells (CD3+) from PBMCs at multiple time points. This dataset is growing as additional time points are collected. Data includes up to 2026-01-13.

Hudson Lab (FASTQ + Seurat + Flow)

• FASTQ: hudson_lab/PBMC_scRNAseq/FASTQ — time points: Jan 2025, Apr 2025, May 2025, Jun 2025, Jul 2025, Aug 2025, Sep 2025, Nov 2025, Dec 2025
• Cell Ranger output: hudson_lab/PBMC_scRNAseq/cellranger
• Seurat objects: hudson_lab/PBMC_scRNAseq/seurat_objects
• Flow data: hudson_lab/flow_data
• Peptide expansion: hudson_lab/peptide_expansion

Data generated by Hudson Lab

Kamil’s PBMC scRNA-seq Analysis (GEX, TCR, CNV, CITE)

Re-analysis of PBMC scRNA-seq data by Kamil, including Cell Ranger multi outputs for GEX, TCRαβ, TCRγδ, and CITE-seq across multiple blood draw time points.

• Cell Ranger outputs: kamil/blood/output — GEX, TCRαβ, TCRγδ, CITE-seq pools for each time point
• Analysis: kamil/blood/analysis — combined CNV (h5ad), TCR clonotype analysis, database matching

Spatial Transcriptomics & Proteomics

Elucidate Bio (Phenocycler Fusion + Visium HD)

Generated by Elucidate Bio. Includes multiplexed IF data with Phenocycler Fusion instrument and custom conjugated antibodies, plus Visium HD run on the same section.

• Data dictionary
• Raw and processed data — elucidate/SIN-01_20250915
• Consolidated proteomics & transcriptomics (h5mu, by segmented cell)

Xenium (10x In Situ)

Xenium in-situ spatial transcriptomics for T0 tissue blocks B3 and C3.

• xenium/T0/output-XETG00279__0078011__B3__20260211__182948 — Block B3
• xenium/T0/output-XETG00279__0078018__C3__20260211__182947 — Block C3
• xenium/cartoscope — Cartoscope visualization output

HMS ORION Multiplex Imaging

ORION highly multiplexed immunofluorescence imaging and Minerva story visualizations.

• hms_spatial/orion — ORION OME-TIFF images
• hms_spatial/minerva — Minerva stories for H&E blocks, ORION, and IHC (B7-H3, EphA2)

Pathology & Imaging

Histopathology slides and immunohistochemistry images. Viewable at osteosarc.com/imaging.

HLA Type

Red Cross HLA typing results.

Class I

Class II

Vaccine Overlap Summary

View the vaccine overlap summary spreadsheet →

Analysis Tools

Shiny App

An R Shiny app compares bulk RNA-seq data to healthy tissues (GTEx) and other cancers (TCGA).

• R code for the Shiny App
• Data referenced in R code

Interactive Visualizations on This Site

• Cell Clusters — single-cell RNA-seq explorer
• GSEA — gene set enrichment analysis
• Treatment Timeline — treatment history, MRD, and flow cytometry
• CNV Browser — copy number variation from WGS
• Imaging — pathology image viewer

Data Access

Google Cloud Bucket

All data is stored in the gs://osteosarc-genomics bucket.

Pattern Unify System (RCRF)

Several datasets are indexed in the RCRF Pattern Unify system for programmatic access.

1. Email unify-admin@rcrf.org to request access.
2. Go to data-commons.rcrf-dev.org and create an account with the same email.
3. Use the patternq Python library to query data.