RNA of 32 GCT samples was sequenced on Illumina HiSeq2000 according to the manufacturer’s protocol (Illumina). 100-bp paired-end reads were assessed for quality and reads were mapped using CASAVA (Illumina). The generated FASTQ files were aligned by Bowtie261 (link) and TopHat262 (link). Cufflinks63 (link),64 (link) was used to assemble and estimate the relative abundances of transcripts at the gene and transcript level. DEFUSE35 (link) was used for fusion gene discovery.
Corresponding Organization : Children's Hospital of Los Angeles
Other organizations :
University of Southern California, SickKids Foundation, University of Toronto, Hospital for Sick Children, Riley Hospital for Children, Yale University, University of Minnesota, Princess Máxima Center, Boston Children's Hospital, Hospital Sant Joan de Déu Barcelona, University of California, Davis, Dana-Farber/Boston Children's Cancer and Blood Disorders Center
Transcript assembly and abundance estimation (Cufflinks)
Fusion gene discovery (DEFUSE)
dependent variables
Transcript abundances at the gene and transcript level
Fusion gene discovery
control variables
RNA samples from 32 GCT (Germ Cell Tumor) samples
controls
No explicit positive or negative controls were mentioned.
Annotations
Based on most similar protocols
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