Chordoma-omics data

The Chordoma Foundation has conducted comprehensive characterization of 21 chordoma cell lines and 12 patient-derived xenograft (PDX) models using Whole Exome Sequencing (WES) (100X, 150bp paired-end) and Whole Transcriptome Sequencing (WTS) (80M reads, 150bp paired-end). Each model underwent WTS on four biological replicates (i.e., distinct PDX tumors or culture dish of cells) across at least two passages to account for gene expression variability.

The raw sequencing data is available for download on Cavatica.

The model sequencing summary data is available on PedcBioPortal.

Instructions on how to access raw sequencing data in Cavatica

Register for an account on Cavatica and request access to the 'Chordoma Foundation Dataset'. Once access is approved, locate the files in the 'Model_Data_Batch_1' and 'Model_Data_Batch_2' subfolders. The most recent RNA-Seq data can be found in the 'Model_Data_Batch_2' folder, specifically within the 'source-data' subfolder.

In navigating Cavatica, the "Sample ID" column denotes the model name, while "Sample Type" indicates either cell line or PDX. The relevant files are categorized under "Experiment Strategy" as RNA-Seq. Each model includes N=4 biological replicate RNA-Seq files, with replicate files labeled R1, R2, R3, R4, or occasionally D1. Note, data for the 21 cell lines and 12 PDXs spans multiple pages.

Here is some information regarding bulk data downloads from Cavatica.

If you require any assistance with data access or navigation, please contact us.