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• Metagenomic sequencing of fecal samples from celiac disease patients and controls

  150 nt paired-end metagenomic shotgun sequencing (Illumina HiSeq 2000) of fecal samples from 130 (mostly treated, i.e. adhering to gluten-free diet) celiac disease patients and 106 controls from the CeDNN cohort from the University Medical Center Groningen, The Netherlands. For six celiac disease patients, data from two timepoints (before and during gluten-free diet) are included, resulting in a total of 242 samples. The dataset includes 2 encrypted fastq files per sample (.fq.gz.c4gh) en sample phenotypes (.txt.c4gh).

  Dataset EGAD50000001397

• RIP-SeqRaw data

  This dataset contains 15 paired FASTQ files from the PTBP1 project. Sequencing data were generated using bulk directional RNA-seq and RIP-seq experiments performed on a NovaSeq 6000 platform (2×100 bp paired-end reads). The dataset comprises two groups of samples: controls and patients. For each group, both input and immunoprecipitated samples are available. Patient samples correspond to skin biopsies from individuals affected by a neurodevelopmental disorder associated with variable skeletal dysplasia and disproportionate short-limbed short stature.

  Dataset EGAD50000001723

• Broad utility of ultrasensitive analysis of circulating tumor DNA (ctDNA) dynamics across solid tumors treated with immunotherapy

  Here, we applied a whole-genome, tumor-informed approach to study ctDNA in more than 202 advanced-stage cancer patients treated at VHIO. This study demonstrates the efficacy of ultrasensitive ctDNA as a broad biomarker in a large pan-cancer discovery and validation cohort, spanning 24 tumor types treated with diverse immunotherapy modalities. It demonstrates ctDNA’s potential for early response assessment, survival prediction, and distinguishing true progression from pseudoprogression, enhancing its clinical relevance. This dataset captures the plasma sequencing data from the project.

  Dataset EGAD50000001813

• Transcriptional data of human isogenic iPSCs

  This dataset contains bulk RNA-seq data from 12 autosomally isogenic human iPSCs. Three biological replicas from XXY (sample ID 419295-7), XX (sample ID 419298-419300), XY (sample ID 419302, 419305-6), and XO (sample ID 419308, 419310, 419312) hiPSC. RNA for this dataset was collected using Trizol method, and polyA library type was implemented. The libraries were sequenced using Illumina device. The sample reads are deposited as fastq files. Analysis have been done using reference alignment to GRCh38 reference genome.

  Dataset EGAD50000001361

• ovarian cancer sample exome seq

  Tissue samples were collected from 18 ovarian cancer patients. After mechanical and enzymatic dissociation, a part of these tissues underwent growth factoromics analysis. For four cases, single-cell sequencing analysis was conducted under conditions with or without estradiol. Additionally, the remains of the tissues were frozen and subsequently subjected to exome sequencing on 16 of these samples. Sixteen cases were diagnosed as HGSOC, while two samples were clear cell or mucinous type (Extended Data Table 1). All cases were grade 3, and none had received neoadjuvant chemotherapy.

  Dataset EGAD50000002057

• Somatic mutation and clonal evolution in the human bladder_WES (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-exome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006115

• Somatic mutation and clonal evolution in the human bladder Novaseq (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-genome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006116

• Detection of Gene Fusions using Targeted Next-Generation Sequencing

  Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).

  Dataset EGAD00001006913

• Dataset for Ewing_sarcoma_PNET-RNA

  Rare cancer sequencing data of 28 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008845

• Sequencing data for oesophageal and related samples - Black et al (WGS)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS OACs/BOs/normals)

  Dataset EGAD00001011187