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• Targeted analysis of chondrosarcoma cancer genes (2019-04-01)

  Targeted analysis of chondrosarcoma cancer genes . This dataset contains all the data available for this study on 2019-04-01.

  Dataset EGAD00001004877

• Pervasive H3K27 acetylation and ERV expression in H3.3K27M gliomas present a therapeutic vulnerability

  We sequenced a total of 2 H3.3K27WT (pcGBM2, G477; 3 replicates total) and 2 H3.3K27M (DIPGVI, DIPGXIII; 6 replicates total) patient-derived cell lines as well as Crispr/Cas9 H3.3K27M-KO clones for one of the cell lines (3 replicates total; DIPGXIII-KO) using ATAC-Seq. P-XX designates passages of replicates. These samples can be found at GEO under accession number GSE128744. This repository contains 1 replicate of G477 to be released under controlled access.

  Dataset EGAD00001004961

• PIVUS study - Longitudinal transcriptomics - Advanced aging

  We performed RNA sequencing in whole-blood from the same 65 individuals from the PIVUS study at ages 70 and 80 (130 samples) to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging. Each individual has four fastq files, two for each age. Consecutive sample IDs refer to the sample individual, e.g. PIVUS003 and PIVUS004 are the age 70 and age 80 samples of the first individual.

  Dataset EGAD00001004965

• Whole-transcriptome sequencing of MPN patients and controls.

  This dataset contains whole-transcriptome sequencing data of 113 myeloproliferative neoplasms (MPN) patients and 15 controls. Patients were diagnosed with essential thrombocythemia, polycythemia vera, primary myelofibrosis, and secondary acute myeloid leukemia. The data were pooled from 5 different sequencing experiments as indicated using an Illumina HiSeq2000 machine. All samples were sequenced paired-end. Sequenced samples were processed with custom workflows for discovery of fusion genes, SNVs and Indels calling, and identification of splicing abnormalities.

  Dataset EGAD00001004788

• RNA-seq data

  This dataset contains 200 RNA-seq bam files (142 SLE, 58 healthy individuals). RNA libraries were prepared with the Illumina TruSeq sample preparation kit and were sequenced on Illumina HiSeq2000. 49 bp paired-end reads were mapped to the GRCh37 reference human genome using the GEM mapper.This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity

  Dataset EGAD00001005037

• Comprehensive single cell study of lung adenocarcinoma from early to metastatic stages

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas and dynamics during lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

  Dataset EGAD00001005054

• NIHR BioResource Rare Diseases WGS project - Ehler-Danlos (ED) and ED-like Syndromes (EDS) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Ehler-Danlos (ED) and ED-like Syndromes (EDS) Rare Disease domain.

  Dataset EGAD00001005123

• Small RNA-sequencing and RNA-sequencing data of tuberous sclerosis complex subependymal giant cell astrocytomas

  This data set contains small RNA-sequencing and RNA-sequencing data from subependymal giant cell astrocytomas (SEGA) resected from tuberous sclerosis complex patients. Small RNA-sequencing and RNA-sequencing were performed on the same set of SEGAs (n=19) and periventricular controls (n=8). For full details on library preparation and patients please refer to the paper "The coding and non-coding transcriptional landscape of subependymal giant cell astrocytomas." (PMID: 31834371 DOI: 10.1093/brain/awz370).

  Dataset EGAD00001005932

• Pediatric Glioblastoma with Persistent STAG2 Mutation

  This case represented the genomic findings of a pediatric glioblastoma patient who underwent multiple surgical resections and treated with standard chemoradiation, as well as a novel recombinant poliovirus vaccine therapy. The results present the preservation of a STAG2 mutated clone, besides elimination and emergence of other clones with oncogenic mutations through disease progression under different treatment modalities. Although STAG2 deficiency comprises only a small subset of gliomas, this case adds clinical evidence to existing preclinical data supporting a role for STAG2 mutations in gliomagenesis and resistance to standard therapies.

  Dataset EGAD00001006202

• WES data from 165 tumor/germline samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). WES was performed using DNA from 165 tumors (76x median coverage) and associated germline DNA (46x median coverage). Data provided here consist of 5,828 fastq files for WES.

  Dataset EGAD00001006239