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• Genomic characterization of germ-cell tumors in childhood

  Germ cell tumors (GCTs) are rare neoplasms affecting approximately 3.5% of pediatric patients, with diverse histological subtypes. Despite their low mutational burden, prevalent alterations in KIT, KRAS, and NRAS genes are observed, but molecular understanding of pediatric GCTs lags behind adult counterparts. We aimed to elucidate the genomic landscape of 16 pediatric GCT patients via whole exome sequencing (WES), which revealed somatic alterations resembling those in adult GCTs.

  Study EGAS50000000619

• Transcriptomic profiling of myeloid cells from secondary lymphoid organs (lymph nodes and tonsils) from lymphoma patients and controls.

  Despite their recognized impact on the pathogenesis and prognosis of B-cell lymphoma, tumor-associated macrophages (TAM) have not been extensively explored in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). We investigated mononuclear phagocyte (MNP) heterogeneity using single cell RNA sequencing (scRNAseq) in B-cell lymphoma lymph nodes compared to reactive secondary lymphoid organs (lymph nodes and tonsils).

  Study EGAS50000001135

• Investigation of chromatin accessibility in clear cell renal cell carcinoma using ATAC-seq

  To identify regions of open and accessible chromatin in clear cell renal cell carcinoma (ccRCC), we performed ATAC-seq on the 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq and processed narrowPeak fomats. Data were processed using the nf-core atacseq pipeline.

  Dataset EGAD50000001885

• ProstOmics - DNA methylation v2

  Bulk methylation array data from 32 prostate tissue samples from 8 patients (3 with post-surgery relapse). Methylation data were acquired using the microarray assay Illumina Infinium MethylationEPIC v2.0 Kit. The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Dataset EGAD50000000606

• ProstOmics - DNA methylation v1

  Bulk methylation array data from 64 prostate tissue samples from 16 patients (5 with post-surgery relapse). Methylation data were acquired using the microarray kit Illumina Infinium MethylationEPIC BeadChip (n=64 ). The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Dataset EGAD50000000605

• Single-cell multi-omics reveals clonal evolution and T-cell dynamics underlying differential responses to ibrutinib in Waldenström macroglobulinemia.

  To elucidate the molecular basis underlying differential response and resistance to ibrutinib in Waldenström’s macroglobulinemia (WM), we conducted a prospective phase II trial (NCT02604511) of ibrutinib monotherapy in treatment-naïve patients. Seventy-four sequential bone marrow (BM) aspirates from 17 patients, collected from baseline through 48 treatment cycles, were profiled using single-cell RNA and V(D)J sequencing.

  Study EGAS50000001596

• Variation and transmission of the human gut microbiota across generations - shotgun data

  Variation and transmission of the human gut microbiota across generations - shotgun sequencing data

  Dataset EGAD00001008207

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - sequence data (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - sequence data (Mutographs)

  Dataset EGAD00001015386

• Molecular characterization of hepatocellular carcinoma in patients with non-alcoholic steatohepatitis

  Patients with hepatocellular carcinoma (HCC) associated to non-alcoholic steatohepatitis (NASH) are increasing globally, but their molecular traits are not well characterized. Our molecular characterization revealed higher rates of ACVR2A mutations (10%) – a potential tumour suppressor, presence of a novel mutational signature (MutSig-NASH-HCC), a more relevant role of Wnt/TGF-β proliferation subclass in tumours (42%) and immunosuppressive traits in the adjacent non-tumoral tissue.

  Study EGAS00001005222

• WTS data of patients diagnosed with angiosarcoma

  Whole-transcriptome sequencing (WTS) of 6 tumor-normal and 6 tumor-only samples from patients diagnosed with angiosarcoma. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.

  Dataset EGAD00001005367