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.

Contents
WGS
- Copy number profiling (PURPLE)
- Somatic variants (Mutect2, Strelka2, vardict)
- Structural variants (GRIDSS, GRIPSS, Linx)
- Telomere quantification (Telomerehunter)

Methylation
- Beta values from Illumina EPIC arrays

Small-RNA-Seq
- Normalised Log2-CPM values
- Raw gene counts (FeaureCounts)

RNA-Seq (Whole transcriptome)
- Normalised Log2-CPM values
- Raw gene counts (HTSeq)
- Fusion detection (Arriba)

Single nuclei ATAC-seq
- Aggregated fragment matrix (CellRanger)

Single nuclei RNA-seq
- Feature count matrices (CellRanger)

Supersets
- Methylation (merged data from A5, TCGA, and GSE43298)
- WTS (merged data from A5, TCGA, and Flynn et al. (2015))
- Small RNA (merged data from A5, TCGA, and Castro-Vega et al. (2015))