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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

• Whole-genome enzymatic DNA methylation sequencing and single-cell RNA sequencing data from nasal cells of COVID-19 patients

  Nasal swabs were collected from COVID-19 patients during the acute phase of infection as well as 3 and 12-months post-infection. Cells isolated from nasal swabs were subjected to whole-genome enzymatic DNA methylation sequencing (n=33) and scRNA-seq (n=24). For n=12 former COVID-19 pateints, follow-up samples were collected at 3 and 12 months post-infection and subjected to scRNA-seq.

  Dataset EGAD50000000398

• ETMR_Nanostring

  Total RNA (100ng) from 21 ETMRs with C19MC structural alterations and 28 other PBTs was prepared with nCounter miRNA Sample Prep Kit according to standard protocol. miRNA expression profiling was conducted with human v1, v2, or v3 miRNA panel on nCounter miRNA expression platform (NanoString Technologies, Seattle, WA) according to manufacturer’s protocol. Signal normalization was done using nSolver Analysis and batch corrected using ComBat (Johnson et al. Biostatistics. 2007). 565 miRNAs overlapped between all three versions and was used for further analyses. Fold change and supervised t-test with FDR correction was calculated between the ETMRs and other PBTs.

  Dataset EGAD00010001701

• 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

• Single cell RNA sequencing of mononuclear cells from synovial fluid of patients with rheumatoid arthritis

  Mononuclear cells were collected from synovial fluid of anti-citrullinated positive antibodies (ACPA)-positive rheumatoid arthritis patients (n=8) and ACPA-negative RA patients (n=8). Global cell types (i.e., no enrichment) were obtained from these cryopreserved synovial fluid mononuclear cells (SFMC) samples and immediately fixed and processed using the GEM-X Flex Gene Expression Reagent Kits (10x Genomics) according to protocol. Following Gel Bead-in Emulsion (GEM) generation, samples were processed using the standard manufacturer’s protocol. Once sequencing libraries passed standard quality control metrics, libraries were sequenced on an Illumina NextSeq2000 P4 100 cycle reagent kit with the following read structure: R1: 28, R2: 90, I1: 10, I2: 10. Libraries were sequenced to obtain a read depth greater than 10,000 reads/cell for gene-expression (GEX). FASTQ files are made available. More detailed information can be obtained in Argyriou A. et al, Annals of the Rheumatic Disease, 2025.

  Dataset EGAD50000001801

• Viral evasion Strategy for Generating Hypoimmunogenic hiPSC Lines

  Mismatches in HLA haplotypes between donors and recipients significantly increase the risk of graft failure due to immune rejection. To address these limitations, we introduced a cytomegalovirus-derived US2 encoding sequence into the AAVS1 safe-harbor locus of a human induced pluripotent stem cell (hiPSC) line. US2 expression in iPSC abolished HLA-A2 alloreactive T-cell activation without increasing NK cell degranulation, indicating preserved inhibitory signaling.

  Study EGAS50000001618

• High hyperdiploid ALL single cell whole genome sequencing

  This dataset was collected from viable bone marrow cells obtained at diagnosis from nine patients with high hyperdiploid ALL and one normal bone marrow sample. All samples were subjected to low pass single cell whole genome sequencing with the median sequencing coverage of 0.02x. Single nuclei in G0/G1 phase were isolated using a fluorescence-activated cell sorting (FACS) cytometer. DNA libraries were constructed and associated next-generation sequencing was carried out by European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. Further details regarding the DNA libraries construction are available by Bos et. al., 2019 (https://link.springer.com/protocol/10.1007/978-1-4939-8931-7_15).

  Dataset EGAD00001008988

• Genomic profiling of BRCA- mutant breast cancer tumors

  This data set contains whole exome sequencing (WXS) and RNA-Seq on germline BRCA- mutant tumors from 18 patients. BAM files are provided for WXS on tumor and germline samples. FASTQ files are provided for the RNA-Seq samples. Sequencing was done on an Illumina Hi-Seq 2500.

  Dataset EGAD00001008276

• Genetic regulation of RNA splicing in human pancreatic islets

  Here we provide access to newly generated RNA-seq data for 101 human islet samples used to map genetic effects on gene expression and alternative splicing (eQTLs and sQTLs) in a total of 399 human islets. We also make publicly available genotyping array data for 128 human islets, including the fraction of 101 human islet samples with existing RNA-seq data.

  Dataset EGAD00001009102

• Epigenetic profiles of neuroblastoma PDXs

  This dataset contains bam files for ChIP-seq experiments for 6 neuroblastoma PDXs (Patient Derived Xenograft). It includes the bam files for the H3K27ac mark as well as the bam files of the corresponding input DNA for each sample.

  Dataset EGAD00001003394