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• Genetic landscape of pediatric Low Grade Gliomas & Glioneuronal tumors

  We performed whole-genome sequencing of 42 paired tumor/normal LGG genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000255

• Whole-Transcriptomic Profiling of Sorted Human Renal Cell Carcinoma Immune Populations

  It is poorly understood how the tumor immune micro-environment influences disease progression in renal cell carcinoma (RCC). Here we performed whole-transcriptomic profiling of immune cell populations which were derived from RCC patients representing distinct flow-sorted immune lineages.

  Study EGAS00001006593

• Fusion gene analysis using multiplex single primer extension-based RNA-sequencing

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains fusion gene analysis using multiplex single primer extension-based RNA-sequencing for a subset of 25 patients of the screening cohort. Data was generated on Illumina NexSeq 550 device in paired-end mode and is stored in compressed FASTQ file format.

  Dataset EGAD00001011326

• Single circulating tumor cells in hepatocellular carcinoma

  We determined intra- and inter-vascular transcriptional heterogeneity within the circulatory system using single-cell RNA-sequencing of 113 CTCs isolated from four key vascular sites along their dissemination route in ten HCC patients. The dataset consists of 146 paired-end fastq files from 113 sigle CTCs, HuH-7 cell line, Hep3B cellline, white blood cell, tumor and normal bulk tissue.

  Dataset EGAD00001007642

• Single-cell Transcriptomic and Immune Receptor Profiling of PBMCs from Dengue-Infected Individuals with Varying Disease Severities

  This dataset comprises single-cell RNA sequencing (scRNA-seq) and immune receptor (TCR/BCR) profiling of peripheral blood mononuclear cells (PBMCs) collected from individuals infected with dengue virus (DENV) exhibiting different clinical severities: asymptomatic dengue (AD), dengue fever (DF), and dengue hemorrhagic fever (DHF). PBMCs were collected during the acute phase and, in some cases, during convalescence. The data provide a resource for understanding protective versus pathogenic immune responses in dengue infection.

  Dataset EGAD00001015634

• Non-invasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA

  This dataset contains a total of 10 families and 51 samples presented in 'Non-invasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA' study, in which 9 of them are cfDNA samples and the rest of samples are gDNA samples. All the samples are targeted sequencing data with a custom 45Mb capture library . Raw pair-end fastq files for each sample is available.

  Dataset EGAD00001004989

• Capture Hi-C on Hodgkin lymphoma

  In situ promoter capture Hi-C on Hodgkin lymphoma cell line L-428 in experimental triplicates. Hi-C libraries were prepared as previously described (Orlando et al., 2018, https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cphg.63). Promoter capture was based on 32,313 biotinylated 120-mer RNA baits (Agilent). Hi-C libraries were sequenced using Illumina HiSeq 2000 technology. The files are in FASTQ format.

  Dataset EGAD00001004321

• sWGS of matched patient and PDX ovarian tumour tissues

  This dataset contains 8 .bam files of shallow WGS (~0.1×) from fresh frozen tumour tissues of four matched patients and first generation PDX models. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008650

• Timing the Philadelphia chromosome and trajectory to chronic myeloid leukaemia

  We sequence >1000 whole genomes from 9 patients with CML, providing the largest sequencing dataset for this cancer. We reconstruct phylogenetic trees using somatic mutations and infer BCR::ABL1 timing and tumour growth rates. We correlate mutation landscapes and clonal trajectories with clinical features.

  Dataset EGAD00001015353

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW20_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_F

  Dataset EGAD00001001797