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• PROJET DREPANOCYTOSE ET PALUDISME

  The goal is to study and specify the response to treatment against Plasmodium falciparum malaria in subjects with sickle cell disease in order to propose to the National Malaria Control Program of Côte d'Ivoire effective prevention and treatment strategies for this population at risk.

  Study EGAS00001006008

• TenK10K Phase 1: Whole Genome Sequencing tandem repeats multi-sample VCFs

  Tandem repeat variants were called for 1,925 samples from phase 1 of the TenK10K project. Variant calling from WGS alignments to the GRCh38 reference assembly was completed with ExpansionHunter v5. This dataset is comprised of autosomal tandem repeat variants provided as multisample compressed VCF format files. SNV-derived principal component scores used in the manuscript (Tanudisastro et al.) are also provided in this dataset.

  Dataset EGAD50000002378

• stem cell-derived beta cells from cell lines RC9 and HUES8

  stem cell-derived beta cells differentiated using two different cell lines: HUES8 (non-clinical grade) and RC9 (clinical grade). iPSC stem cell lines were differentiated to pancreatic islets using differentiation protocol as detailed by Rajaei et al. (2025, Science Translational Medicine, accepted for publication). scRNAseq was done at stage 7 of differentiation (day 30) using 10X genomics 3' sequencing. Cells were annotated then subsetted for beta cells for downstream analysis

  Dataset EGAD50000001322

• RNAseq from 6 organotypic co-cultures (OC cells bulk/OCSC with or without TME)

  The dataset contains samples of 6 organotypic co-cultures, assembled with patient-derived material from ovarian cancer (OC) patients. Tumor cells, both as bulk and as cancer stem cells-enriched (OCSC) populations, are cultured or not with in vitro peritoneal TME (for details see Battistini C et al, Tumor microenvironment-induced FOXM1 regulates ovarian cancer stemness, CDDis 2024). Dataset is composed by fastq file (paired end) type from bulk RNA-Seq.

  Dataset EGAD50000000523

• Single-cell RNA-seq of immune cell subsets isolated from human tumors (Kaptein et al., 2024)

  Single-cell RNA-seq profiling of effector (KLRG1+ PD1-), transitional (KLRG1+ PD1-intermediate), dysfunctional (CD39+ PD1+) and memory (IL7Rα+) CD8 T cells isolated from 4 human tumors (1 melanoma, 1 renal carcinoma and 2 ovarian carcinoma). Respective cell populations were identified and isolated using FACS. FASTQ files contain gene expression data, feature barcode antibody capture or TCR data on individual CD8 T cell subsets across the 4 different samples.

  Dataset EGAD50000000376

• Next generation sequencing on cardiac samples in Hungarian patients of dilated cardiomyopathy

  Heterozygous (HET) truncating mutations in the TTN gene (TTNtv) encoding the giant titin protein are the most common genetic cause of dilated cardiomyopathy (DCM). We investigated 127 clinically identified DCM human cardiac samples with targeted sequencing using the TruSight Cardio panel on an Illumina MiSeq system with a special focus on TTNtvs. This dataset belongs to the publication of Kellermayer, D et al. Truncated titin is integrated into the human dilated cardiomyopathic sarcomere

  Dataset EGAD50000000066

• Clonal expansion of mutated cell population in bladder urothelium

  1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference.

  Dataset EGAD00001003250

• Cancer gene panel (T200.1) sequencing analysis of adult type ovarian granulosa cell tumors (Validation cohort from Hillman, et al)

  Cancer gene panel (T200.1) sequencing data from tumor/normal pairs for adult type ovarian granulosa cell tumor sequencing project. This data set contains 55 tumor panel sequencing data and 44 matched normal panel sequencing data generated using the MD Anderson Cancer Center T200.1 cancer gene hybrid capture platform, with sequencing performed on an Illumina HiSeq 2000. This dataset contains BAM files generated by aligning paired-end reads to the hg19 reference genome.

  Dataset EGAD00001004091

• miRNA data for aSAH patients with or without subsequent vasospasm

  These files contain the normalized and raw count abundances miRNA for aSAH patients. These abundances were obtained using Next-Generation Sequencing after selection of the miRNA in the RNA biobank. In total, there are 28 VSP- and 28 VSP+ patients for two-time points. Normalized data were obtained by applying size factor and VSN normalizations as described in Pulcrano-Nicolas et al. Stroke 2018. Raw count data corresponding to the raw abundances of miRNA in aSAH patients.

  Dataset EGAD00001004185

• Contribution of Retrotransposition to Developmental Disorders

  Variants and WGS data for Gardner et al. 2018 (biorxiv 471375). One VCF each for Alu, L1, and SVA. Flat text file and WGS for processed pseudogenes.

  Dataset EGAD00001004586