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Profiling RNA Translation in Pediatric Medulloblastoma
dbGaP
Data Resource:  dbGaP
Point of Contact:  
John Prensner,  
Project

About This Dataset
This study provides RNA-sequencing and ribosome profiling data for patient-derived cell lines and patient tissue samples for children with medulloblastoma. Ribosome profiling is a variant protocol of RNA-sequencing that directly sequences ribosome-bound RNA fragments only. Samples were processed for poly-A mRNA sequencing using the Roche Kapa Kit. These data were used to quantify P-sites of open reading frames. RNAseq and ribo-seq data were integrated and compared to determine translational efficiency values using TPM (Ribo-seq) over TPM (RNA-seq) as the metric. Ribo-seq data on 14 samples and RNAseq data on 21 samples derived from 16 fresh-frozen surgical samples for medulloblastoma and 5 autopsy samples are available through dbGaP. A second cohort of 4 medulloblastoma samples (RNAseq, Ribo-seq) related to this study can be found on the EGA at EGAS00001007426.
Core Data Elements
Number of Cases
21
Case Sex
Unknown (21)
Case Age At Diagnosis
Pediatric and Young Adult (<40 years) (21)
Case Race
Not Reported (21)
Case Ethnicity
Not Reported (21)
Case Disease Diagnosis
Pediatric Medulloblastoma (21)
Case Tumor Site
Brain (21)
Number of Samples
57
Sample Analyte Type
Other (16); RNA (41)
Sample Anatomic Site
Brain (57)
Sample Is Normal
Yes (2); No (55)
Additional Data Elements
DBGAP STUDY IDENTIFIER
SRA STUDY IDENTIFIER
Grant Information
K08CA263552-01A1
Deciphering non-canonical translation in high risk medulloblastoma
Published In
https://doi.org/10.1101/2023.05.04.539399
Charts
Unknown (21)
21Unknown