Cancer Cell. Volume 29, Issue 3: p.394-406, 14 March 2016, 10.1016/j.ccell.2016.02.009
Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs. Our analyses revealed gene expression and methylation subgroups and focused on dysregulated pathways, including those involved in neural crest development.
This study characterized TARGET cases as described below:
| 40 Discovery Cases | 29 Validation Cases | |
|---|---|---|
| 40 cases had mRNA-Seq | 25 cases had mRNA-Seq | |
| 40 cases had miRNA-Seq | 26 cases had miRNA-Seq | |
| 40 cases had WGBS | 29 cases had WGBS | |
| 40 cases had methylation array | 28 cases had methylation array | |
| 16 cases had ChIP-Seq | 19 cases had ChIP-Seq | |
| 40 cases had WGS | 29 cases had WGS |
WGBS = Whole genome bisulfite sequencing, methylation array = Illumina’s Infinium MethylationEPIC (850K)
In order to access Controlled TARGET RT data using the links below, users must submit an application for Authorized Access via dbGaP as described on dbGaP’s TARGET Study Page. To begin the application process, please view the information and instructions provided on the dbGaP Authorized Access Login Page under “dbGaP Data Download”.
Supplemental Data Files
- GDC Manifests
- Controlled-Access Data Download Manifest (5 Files)
- Open-Access Data Download Manifest (10 Files)
- mRNA-Seq
- TARGET RT mRNA-Seq Level 3 Data
- TARGET RT mRNA-Seq Level 3 Data (Controlled)
- TARGET RT mRNA-Seq Metadata
- miRNA-Seq
- Bisulfite-Seq
- TARGET RT Bisulfite-Seq Level 3 Data (Controlled)
- TARGET RT Bisulfite-Seq Metadata
- ChIP-Seq
- TARGET RT ChIP-Seq Level 3 Data (Controlled)
- TARGET RT ChIP-Seq Metadata
- Methylation Array
- TARGET RT Methylation Array Level 1 Data (Controlled)
- TARGET RT Methylation Array Level 2 Data
- TARGET RT Methylation Array Metadata
- WGS
- TARGET RT WGS Level 3 Data (Controlled)
- TARGET RT WGS Metadata
- Miscellaneous Files
Additional Resources
- SRA - SRP012000 (link is external) NCBI
Instructions for Data Download
Open Access Data
- Download the appropriate manifest file from the publication page
- Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
- GDC DTT (Download, User's Guide)
- GDC API (User’s Guide)
Controlled Access Data
- Download the appropriate manifest file from the publication page
- Download a token from the GDC Data Portal
- GDC Data Portal (Launch, User’s Guide)
- Use the manifest file and token to download data using the GDC DTT or the GDC API
- GDC DTT (Download, User’s Guide)
- GDC API (User’s Guide)
For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io