🔬 Explore Sid's Data

Treatment Timeline

Interactive visualization of treatment history, MRD measurements, procedures, and imaging from November 2022 to present.

Bulk RNA-seq

Interactive explorer for bulk RNA-seq gene expression across multiple assays (BostonGene, Tempus, Personalis) with GTEx and PCAWG comparisons, copy number context, and single-cell overlays.

scRNA-seq

Single-cell RNA-seq from:

• Tumor biopsies at time points T1, T2, and T3
• CD3+ PBMC at eight time points

Gene Set Enrichment Analysis

GSEA of the single-cell RNA-seq data from tumor. Limma and DESeq2 results from two levels of cell clusters from tumor single-cell RNA-seq from T1, T2, and T3.

Images

12 images of tissue specimens from osteosarcoma samples.

Vaccine Neoantigen Overlap

UpSet plot of neoantigen mutations across five personalized cancer vaccines (mRNA, JLF V1–V3, CeGaT) with variant allele frequency trends and ELISPOT results.

Copy Number Variation

Interactive genome browser showing ASCAT copy number analysis from whole genome sequencing at two timepoints (T1: June 2024, T2: January 2025).

BAM Browser

Interactive IGV genome browser for viewing aligned sequencing data (BAM/BigWig) across WGS, long-read, single-cell, and RNA-seq experiments.

Cell Lines

Information about osteosarcoma cell lines including HOS, U-2 OS, and CAL-72 with genomic profiles and curated citations.

Data Files

25TB of data: bulk WGS, WES, RNA-seq, scRNA-seq, long-read sequencing (ONT), spatial transcriptomics, imaging (H&E, IHC), and HLA typing.