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• Processed RNAseq data

  This dataset contains log2(TPM + 1) transformed counts for the 823 tumor samples profiled by RNAseq.

  Dataset EGAD00001006618

• Raw FASTq files

  This dataset contains FASTq files for tumors from the 823 patients profiled by RNAseq.

  Dataset EGAD00001006619

• PacBio data of de novo assembly individual EGYPT

  This is the PacBio long read data used for performing de novo assembly of the EGYPT individual (mapped against GRCh38).

  Dataset EGAD00001006034

• RNAseq for brainstem glioma

  RNAseq on Illumina HiSeq X Ten of brainstem glioma primary tumor sample

  Dataset EGAD00001006094

• Melanoma exome profiling

  This dataset includes whole exome profiling of 65 early-passage metastatic melanoma cell lines. The data are provided as BAM files for tumor and normal samples.

  Dataset EGAD00001006271

• 1_fibroblasts_HD_vs_Ctrl_DMSO_Branaplam

  n=4 Ctrl and n=4 HD fibroblasts lines were treated with DMSO or 10nM Branaplam for 72h and RNA-seq was performed.

  Dataset EGAD00001008807

• Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

  We tested the efficiency and reproducibility of 10 RNA isolation methods on 5 different biofluids. Pooled human plasma and serum, bile and urine were used along with cell culture supernatants from human embryonic stem cells (hESC), primary neonatal rat ventricular myocytes (NRVM) and human cholangiocarcinoma cells (KMBC). 4 RNA isolation methods designed to isolate total RNA from bio fluids without enrichment of exRNA carriers were used. 6 methods that preferentially enriched for exRNA carriers were also compared. Small RNA libraries were constructed using the NEBNext small-RNA library prep. The efficiency and reproducibility of the different RNA isolation methods was compared using small-RNA seq.

  Study phs002143

• Sequencing data of multiple sarcoma samples for personalized medicine and endotype identification

  Sequencing data derived from multiple patient samples was used to guide multiple patient-specific experiments and identify potential therapeutic options. These diseases are rare and high-risk (undifferentiated pleomorphic sarcoma, rhabdomyosarcoma) and thus have few available validated clinical options. This leaves the population of patients with few options if, and when, standard therapy fails to cure or control disease. An aspect of the personalize therapy design included the identification of broader disease endotypes (a combination of genetic and clinical data describing patient status) to identify subgroups of the individual disease that could better define treatments and could segment patient populations for deeper preclinical research.

  Study EGAS00001003981

• Massive Genomic Rearrangment Acquired in a Single Catastrophic Event During Cancer Development

  Cancer is driven by mutation. Using Agilent exome hybridisation capture and Illumina GA massively parallel sequencing technology, we aim to sequence ~1600 microRNAs plus the protein coding genome of 25 matched human renal cancer samples. Bespoke algorithms are being developed to identify the somatically acquired point mutations, insertions and deletions in these samples. This project will give unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with renal cancer development.Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00000000029

• Single-nucleus brain transcriptomics reveals microglia dysfunction in Multiple System Atrophy

  Multiple System Atrophy (MSA) is a rare, age-related neurodegenerative disease that shares clinical and pathological features with Parkinson’s disease (PD) but presents a more devastating disease course. To elucidate the distinct cellular pathophysiology underlying multiple system atrophy (MSA) or Parkinson's disease (PD), we performed single-nucleus RNA sequencing on postmortem striatal brain tissue from 7 MSA and 12 PD patients, and 10 non-neurological cases. Using 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1, we isolated 130k nuclei covering all major cell types of the striatum. We performed state-of-the-art bioinformatic analyses on the data followed by orthogonal analyses to validate our findings. We identified a disease-specific activation of microglia cells distinguishing the two diseases and possibly explaining some of the detrimental effects observed in both.

  Study EGAS50000001406