E-MTAB-1367 - RNA-seq of four neuroblastoma patient samples to identify abnormal transcripts expressed in each sample

Status
Released on 3 March 2013, last updated on 3 May 2014
Organism
Homo sapiens
Samples (4)
Protocols (5)
Description
RNA-seq for four neuroblastoma samples (Paired-end protocol). Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we investigated somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries (SRA accession number ERP001414) and RNA-seq. In one cell line and in the two primary tumors, this approach confirmed the localization of the majority of rearrangements within one or two chromosomes, consistent with the phenomenon of chromothripsis. RNA-seq experiments confirmed expression of several predicted chimeric genes and genes with disrupted exon structure including ALK, NBAS, FHIT, PTPRD and ODZ4. RNA-seq analysis allowed the identification of abnormal transcripts expressed from genomic rearrangements that may be involved in neuroblastoma oncogenesis.
Experiment types
RNA-seq of coding RNA, all pairs, co-expression, disease state
Contact
Citation
Genome-wide massively parallel sequencing to characterize genomic rearrangements in neuroblastoma: from unbalanced translocations to chromothripsis. Valentina Boeva, Stephanie Jouannet, Romain Daveau, Valerie Combaret, Cecile Pierre-Eugene, Alex Cazes, Caroline Louis-Brennetot, Gudrun Schleiermacher, Sandrine Ferrand, Gaelle Pierron, Alban Lermine, Thomas Rio Frio, Virginie Raynal, Emmanuel Barillot, Olivier Delattre and Isabelle Janoueix-Lerosey.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1367.idf.txt
Sample and data relationshipE-MTAB-1367.sdrf.txt
Links