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• Whole exome sequencing of Ewing sarcoma and CIC-DUX4 sarcoma

  Whole exome sequencing of a collection of 6 Ewing sarcoma and 3 CIC-DUX4 sarcoma tumoroids plus 4 matched patient tumors and normal tissue. Tumoroids were established from digested patient tumor material as 3D culture in Matrigel. After 2-3 month of growth, Genomic DNA was isolated from individual tumoroid models using the DNeasy Blood & Tissue Kit (Qiagen) and used for whole exome sequencing. Genomic DNA from corresponding patient tumors and matched normal tissue was tested in parallel, if available.

  Dataset EGAD50000000556

• Transcriptome analysis of patient-derived Schwann cells isolated from human sural nerve biopsies

  This dataset contains the transcriptome analysis of human Schwann cell cultures obtained from sural nerve biopsies from six patients with polyneuropathies (N=3/patient, totalN=18) as well as the nerve fascicles from where they were isolated (N=1/patient, totalN=6). In addition, this dataset includes 8 samples out of commercial human Schwann cell cultures and one sample of a fibroblast culture, which serve as controls for further analysis.

  Dataset EGAD50000001021

• Small RNA-Seq of MicroRNA's in extracellular vesicles of Ushers Syndrome patients

  Small RNA-Seq dataset of MicroRNA's found in tear extracellular vesicles (EVs) and hiPSC-derived retinal pigment epithelium (RPE) cells of Ushers Syndrome patients and control samples. 14 samples were isolated and assessed for quality before preparing libraries using the miReasy and TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating paired end FASTQ files.

  Dataset EGAD50000001709

• Single cell data from TB patients

  The dataset comprises single-cell RNA sequencing (scRNA-seq) data derived from around 60,000 PBMCs collected from donors across different severity groups of extrapulmonary tuberculosis (EPTB) and healthy controls (3 healthy, 3 mild, 3 intermediate, 3 severe). The data include both transcriptomic and surface protein expression profiles obtained using the BD Rhapsody Single-Cell Multiomics System. Libraries were prepared for whole transcriptome analysis (WTA), AbSeq, and sample tagging, with sequencing performed on a NovaSeq 6000 system.

  Dataset EGAD50000001118

• PHRT longitudinal ovarian cancer dataset

  High-grade serous ovarian cancer presents significant challenges due to its poor prognosis and high heterogeneity, both of which complicate treatment responses. This project aims to understand intra-patient tumor evolution by investigating different sampling sites (primary and metastatic) at the time of diagnosis and during disease recurrence. A total of 183 biopsies from 50 patients were collected for this purpose, and bulk mRNA sequencing was performed. The majority of samples originated from following tissue types: omentum, ovary, and ascites.

  Dataset EGAD50000002064

• Bulk RNA sequencing of 36 multi-region IPMN–PDAC tumours comprising 160 sequencing runs

  This dataset contains bulk RNA sequencing data generated from 36 multi-region tumour samples obtained from patients with intraductal papillary mucinous neoplasms (IPMN) and associated pancreatic ductal adenocarcinoma (PDAC). A total of 160 sequencing runs are included. Libraries were prepared from poly(A)-selected RNA and sequenced on an Illumina platform. The data are provided as raw sequencing files for downstream transcriptomic analyses.

  Dataset EGAD50000002215

• Aligned FOS RNA sequencing data

  Total RNA-sequencing Paired-End was performed by GenomeScan (Leiden, the Netherlands) on the NovaSeq6000 platform for full-length FOS (FOS FL), truncated FOS (FOSΔ), a FOS isoform with an L376N mutation (FOS mut), untransduced fMSC (unt) and fMSC with empty pLV (pLV) at week 0, 1, 2, and 3 in triplicate (total of 60 samples). Raw RNA-seq data were processed by the RNA-seq BioWDL pipeline pipeline version 5.0.0 developed by the SASC team at LUMC, LUMC, Leiden, the Netherlands).

  Dataset EGAD50000001839

• Raw and processed snRNAseq data of Choroid Plexus Tumors

  This dataset contains raw sequencing and processed data of single nuclei transcriptomes. The data were generated with 10x chromium probe-based single-nucleus assay on FFPE tissues of 43 Choroid Plexus Tumour resections and 12 non-neoplastic fetal and adult ChP resections. Raw data contain BAM files of the sequencing. Processed data contain count matrices as generated by 10x CellRanger for raw and filtered running options.

  Dataset EGAD50000002320

• TenK10K Phase 1: scRNA-seq fastq format sequencing data

  Single cell RNA-sequencing data for PBMCs from the Tenk10k Phase 1 cohort (1925 individuals post-QC). Libraries were prepared using the 10x Genomics 3’ Chromium Next GEM Single Cell HT V3.1 kit and sequenced on the NovaSeq 6000 platform. This analysis consists of 4,768 fastq format files in 1,192 runs, and an analysis which provides the relationship of 298 library pool samples to 1,925 individual samples.

  Dataset EGAD50000002517

• Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation

  Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation and subsequent analysis of potential therapeutic mechanisms associated with the patient's rare germline mutation. Patient sampels were sequenced from an initial biopsy and from a relapse biopsy, in addition to normal blood as the matched normal DNA. RNA sequencing was performed on the relapse sample as initial sample was unable to produce usable RNA for analysis.

  Dataset EGAD00001006125