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• WGS data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors - MUMC

  The dataset includes cram files from WGS of 2 NEN tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue from the corresponding patients are included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.

  Dataset EGAD00001009988

• RNAseq and ATACseq data

  RNAseq and ATACseq data for the FMF patients and healthy control. The RNAseq data was sequenced on a BGI MGI G400 machine, with PE100 reads. ATAC-seq libraries were prepared with Illumina Nextera primers and sequenced on NovaSeq 6000 platform with 50bp paired-end sequencing, where each sample was sequenced to approximate 60 million reads.

  Dataset EGAD00001010304

• Oxidative phosphorylation is a key ontogenetic feature of monocyte immunometabolism promoting myeloid differentiation after birth

  The dataset consists of 12 samples of monocytes, which were analyzed using RNA-sequencing (RNA-seq). These samples were categorized into four distinct groups, each comprising three samples. The dataset was designed to investigate the transcriptomic and metabolic profiles of monocytes across different age groups and stimulation conditions. 3 neonatal controls, 3 neonatal LPS stimulated, 3 adult controls and 3 adult LPS stimulated samples.

  Dataset EGAD00001011340

• Single-cell RNA and TCR sequencing of 37 PBMC pools of advanced HCC patients.

  scRNAseq and scTCRseq of serial peripheral blood mononuclear cell (PBMC) samples (n=72) taken at various timepoints before and during treatment (Week 0 (W0), Week 3 (W3), Week 6 (W6)). PBMC samples were pooled together into 37 pools, loading 2 or three samples per lane in the 10X Genomics chip, in equal proportions, according to a pre-designed pooling matrix.

  Dataset EGAD00001011345

• RNAseq Atlas in HCC tumors

  The atlas provides a comprehensive exploration of genetic and transcriptomic landscapes within HCC, offering insights into key genomic alterations and gene expression patterns. The integration of DNA sequencing and RNAseq data enhances our understanding of the molecular complexity underlying HCC, potentially paving the way for targeted therapeutic strategies and biomarker discovery in the context of hepatocellular carcinoma.

  Dataset EGAD00001015341

• To profile the landscape of sebaceous tumours_RNAseq

  Sebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract RNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted RNA will be used for RNA sequencing.

  Dataset EGAD00001015368

• RNA-seq data of Metabolic profiling of patient-derived organoids reveals nucleotide synthesis as a metabolic vulnerability in malignant rhabdoid tumors

  Patient-matched normal kidney organoid (103H) and MRT tumoroid (103T2) models were treated for 24h with either DMSO (ctrl), 400nM MTX, or 50nM BAY to investigate the direct effects of drug treatment on the expression of key metabolic enzymes in the nucleotide biosynthesis pathways.

  Dataset EGAD00001015391

• MethylScan data from tissue samples

  Raw data (fastq files) for tumor/normal paired samples (378 samples in total; 78, 58, 29, 24 pairs from liver, lung, ovary, and stomach cancer patients, respectively) profiled with the MethylScan assay, a low cost assay for profiling methylation. The MethylScan assay is designed for cfDNA methylome sequencing that enriches for the disease-associated DNA by depleting background signal. For solid tissues, the assay was performed without the MSRE digestion step.

  Dataset EGAD00001015685

• Immunogenomics of Malignant Brain Tumors

  We performed systematic and comprehensive multi-sector immunogenomic analyses on 93 samples from a cohort of 30 patients with primary or recurrent gliomas or metastatic brain tumors, representing the largest cohort of these brain cancers studied spatially to date. For each patient, we characterized multiple spatially distinct regions using whole-exome (WES), custom capture validation, RNA, and TCR-sequencing. Our findings underscore the significant differences in clonal architecture between gliomas and metastatic brain tumors which translates into distinct neoantigen landscapes and, in turn, tumor infiltrating T cell clonotypic diversity. These data therefore provide high resolution insights into the immunogenomic landscapes within malignant brain tumors which may inform tumor-specific therapeutic approaches.

  Study phs002612

• Metformin for Oral Cancer Prevention

  The M4OC-PREVENT clinical trial addressed whether metformin has utility in the prevention of oral cancer. It is a phase IIa clinical trial of metformin ER 2,000 mg per day given for 12-14 weeks to individuals with oral premalignant lesions, either oral leukoplakia or erythroplakia (which are precursors to oral cancer). The goal was to determine if metformin decreases the size of oral leukoplakia (clinical response). Additionally, effects on biomarkers of cancer risk and metformin effect were ascertained. The clinical trial was performed at the University of California San Diego Moores Cancer Center, the University of Minnesota, and the British Columbia Cancer Agency, with monitoring and oversight provided by the University of Arizona.

  Study phs002437