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• RNA fastq files and mutation annotation files

  This dataset contains the results of both RNA sequencing and DNA sequencing. For RNA sequencing, it includes data from 12 samples derived from 9 patients, provided as raw sequencing files in FASTQ format. For DNA sequencing, it contains mutation information obtained from targeted panel DNA sequencing, including data from 35 individuals in the mutation annotation file (MAF) format.

  Dataset EGAD50000001768

• RNAseq

  Libraries for sixty-eight cases (23 EATL and 45 MEITL) were prepared starting from 1 µg of total RNA using the TruSeq Stranded total RNA Gold kit from Illumina (San Diego, California, USA) and were sequenced in three batches on a HiSeq 4000 machine from Illumina with an average output of 63 million reads per sample (range 49-126).

  Dataset EGAD50000001619

• WGS

  A genome-wide approach based on next generation sequencing (NGS) is performed on trios ( Patient+ Father + Mother) with SAID in order to identify known and new gene variants associated with certain forms of the disease. Whole-genome sequencing (WGS) was performed on frozen PBMCs. DNA was extracted using Chemagic Prime ( Perkin Elmer) and quantified with nanodrop. The raw sequencing data is generated on the Novaseq 6000 using an S4 flowcell, with a sequencing depth of ~30X

  Dataset EGAD50000002026

• Sequencing data from the study "Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer"

  This dataset consists of 71 whole-genome samples and 47 RNA-seq samples. All WGS samples are provided in .bam format and RNA-seq samples are provided as .fq.gz (paired-end). Next-generation sequencing data on whole genomes were processed by aligning sequencing reads to a reference genome (NCBI build 37/hg19) using bwa-mem (0.7.13-r1126).

  Dataset EGAD50000001978

• Clinical data of liver cancer patients from EuCanImage - Use case 1 Synthetic

  This study is part of EuCanImage project. It contains the standardized clinical information following FHIR model. The data was collected together with MRI of patients diagnosed with liver cancer (HCC) and controls (non-HCC). All data is synthetic.

  Study EGAS50000001444

• A study on personalized medicine in genitourinary cancers using genetic biomarkers

  We present a patient with MSI-high castration-resistant PC who showed a remarkable and durable response to pembrolizumab. Whole exome sequencing revealed approximate tumor mutation burden of 61 mutations/Mb as well as biallelic loss of MSH2.

  Study JGAS000510

• Transcriptome analysis of Familial dysautonomia patient cells treated with splice-regulating compounds

  In order to investigate familial dysautonomia patient fibroblasts in response to splice-regulating compounds, cells were treated with RECTAS or TG003 and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

  Study JGAS000170

• exploration of biomarkers in colorectal cancer

  Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. To understand the molecular basis of colorectal cancer, we performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 45 colorectal cancers.

  Study JGAS000489

• DNA methylation array analysis of pediatric T-cell acute lymphoblastic leukemia

  Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is rare and its pathogenesis is poorly understood. To investigate epigenetic profiles of pediatric T-ALL, we performed DNA methylation array analysis in 79 cases of pediatric T-ALL.

  Study JGAS000138

• Transcriptome analysis of Fabry disease iPSC-derived cardiomyocytes treated with splice-regulating compound; RECTAS

  In order to investigate transcriptome profiles in response to splice-regulating compounds, iPSC-derived cardyomyocytes were treated with RECTAS and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

  Study JGAS000225