Multi-omic analysis of 94 PCPG

This archive contains somatic (non-identifiable) data from multi-omic analysis of 94 pheochromocytoma/paraganglioma from 79 patients using six molecular methods including: whole-genome sequencing (WGS) of tumour and matched blood (n=94), whole transcriptome sequencing (RNA-seq) (n=91), small-RNA seq (n=90), DNA methylation profiling (n=93). Droplet-based (10x) single nuclei (sn)RNA-seq and snATAC-seq was applied to 9 and 7 cases, respectively.<br><br>Contents<br>WGS<br>- Copy number profiling (PURPLE)<br>- Somatic variants (Mutect2, Strelka2, vardict)<br>- Structural variants (GRIDSS, GRIPSS, Linx)<br>- Telomere quantification (Telomerehunter)<br><br>Methylation<br>- Beta values from Illumina EPIC arrays<br><br>Small-RNA-Seq<br>- Normalised Log2-CPM values<br>- Raw gene counts (FeaureCounts)<br><br>RNA-Seq (Whole transcriptome)<br>- Normalised Log2-CPM values<br>- Raw gene counts (HTSeq)<br>- Fusion detection (Arriba)<br><br>Single nuclei ATAC-seq<br>- Aggregated fragment matrix (CellRanger)<br><br>Single nuclei RNA-seq<br>- Feature count matrices (CellRanger)<br><br>Supersets<br>- Methylation (merged data from A5, TCGA, and GSE43298)<br>- WTS (merged data from A5, TCGA, and Flynn et al. (2015))<br>- Small RNA (merged data from A5, TCGA, and Castro-Vega et al. (2015))