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• Extraembryonic tissue and cytotrophoblast epigenome mapping

  Maps of H3K27ac from normal 2nd- and 3rd-trimester cytotrophoblasts, preterm severe preeclampsia cytotrophoblasts, and 2nd-trimester amnion. Maps of H3K27me3, H3K27me3, H3K36me3, and H3K4me1 from 2nd- and 3rd-trimester cytotrophoblast. Maps of H3K9me3 from 2nd- and 3rd-trimester cytotrophoblast, smooth chorion, and basal plate. RNA-seq from 2nd- and 3rd-trimester cytotrophoblasts.

  Dataset EGAD00001006066

• Neuron-specifc methylome analysis of Alzheimer's disease brain

  Neuron-specific methylome analysis of Alzheimer's disease brain to detect epigenetic changes related to the pathomechanism.

  Study JGAS000125

• WES bam files associated with HNSCC patients in the LIONESS study

  This dataset contains 85 WES bam/bai files of HNSCC cancer patients as part of with the LIONESS study

  Dataset EGAD50000001487

• 30X_WGS_sequencing_of_100_individuals_from_the_general_Greek_population

  This project entailed generation of high depth WGS (30x) of 100 individuals from the general Greek population.

  Study EGAS00001000988

• Genomic characterization of aggressiveness in pituitary neuroendocrine tumors (PitNETs)

  RNA sequencing data of 227 samples of PitNETs in the context of the genomic characterization of aggressiveness of PitNETs

  Dataset EGAD50000002050

• Angiosarcoma follow-up 2 validation study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Dataset EGAD00001000679

• WGBS data set used in the study, 96 samples

  WGBS data set used in the study, 96 samples

  Dataset EGAD00001007968

• Live slow-frozen human tumor tissues scRNA

  Bam files of 17 samples from 11 different patients. The scRNAseq data were obtained using the 10X 3' Gene Expression kit.

  Dataset EGAD00001009284

• FOCUS Trial

  We studied patients with advanced colorectal cancer, starting treatment with non-curative intent. 2135 unpretreated patients were randomly assigned to three treatment strategies in the ratio 1:1:1. Strategy A (control group) was single-agent fl uorouracil (given with levofolinate over 48 h every 2 weeks) until failure, then single-agent irinotecan. Strategy B was fl uorouracil until failure, then combination chemotherapy. Strategy C was combination chemotherapy from the outset.

  Study EGAS50000000725

• glioblastoma and glioblastoma stem cells (GSCs), RNA-seq and WGS

  Characterization of glioblastoma tumors and glioblastoma stem cells (GSCs) lines via RNA-seq and/or WGS profiling.

  Study EGAS00001004395

• Defective homologous recombination in HCC

  Backgrounds and Aims: We performed an in-depth examination of pathogenic germline (PGVs) and somatic variants in DNA damage response (DDR) genes in hepatocellular carcinoma (HCC) to explore their clinical and genomic impacts. Approach and Results: We used a merged whole exome or RNA sequencing dataset derived from in-house (n=230) and TCGA (n=362) databases of multiethnic HCC samples.

  Study EGAS00001006599

• Single-Cell RNA-Sequencing of Tumor and Immune Cells from Patients with Asymptomatic Waldenstrom's Macroglobulinemia

  We performed single-cell RNA-seq on tumor and immune cells from 30 patients with IgM Monoclonal Gammopathy of Undetermined Significance (IgM MGUS), Smoldering Waldenstrom's Macroglobulinemia (SWM), and overt Waldenstrom's Macroglobulinemia (WM) to identify tumor-intrinsic and immune biomarkers of disease progression in patients with asymptomatic WM. We identified subtypes within MYD88-mutant WM that are associated with clinical presentation and/or patient outcomes. We also characterized immune dysregulation in patients with asymptomatic WM, and demonstrated disordered interferon stimulation in T and NK cells of patients.

  Study phs003787

• RNASeq of PDX and CDX tumours treated with ADC

  Enapotamab vedotin (EnaV), an antibody-drug conjugate (ADC) targeting AXL, effectively targets tumors that display insensitivity to immunotherapy and/or tumor-specific T cells in several melanoma and lung cancer models. Mechanistically, EnaV treatment induced an inflammatory response and immunogenic cell death in tumor cells, and promoted induction of a memory-like phenotype in cytotoxic T cells. Combining EnaV with tumor-specific T cells proved superior to any treatment alone in models of melanoma and lung cancer, and increased ICB benefit in models otherwise insensitive to anti-PD-1 treatment.

  Study EGAS00001004562

• Targeted sequencing data and shallow whole genome sequencing data of Follicular lymphoma.

  Contain data of 2 studies 1: 82 nodal stage 1 FL cases and 139 stage III/IV cases 2: 44 watch and wait stage III/IV and 46 Immediate treatment stage III/IV targeted sequencing data of 369 genes and 12 translocation regions whole genome shallow sequencing data

  Study EGAS00001005755

• Facioscapulohumeral dystrophy transcriptome signatures correlate with different stages of disease and are marked by different MRI biomarkers

  This project includes RNA-sequencing data from human FSHD and control skeletal muscle biopsies. This project includes data from 28 FSHD patients (total 37 samples, including vastus lateralis and tibialis anterior muscles) and 12 control individuals (total 24 samples, including vastus lateralis and tibialis anterior muscles).

  Study EGAS00001005782

• Next-generation sequencing data derived from patient single cells or clonal colonies

  The following samples were generated from the patient samples used in the study: - Bulk DNA sequencing specifically targeting mutated sites of interest derived from clonal cell populations (288 monoclonal colonies - 2 replicates). - Targeted Muta-seq method (Patient P342: 2208 cells, Patient HRK: 1066 cells, Patient LAK: 618 cells, Patient P101: 1080 cells) - Smart-seq2 method (Patient P342 - 768 individual cells).

  Dataset EGAD00001006228

• Paired RNA-Seq data from 17 samples of different tumors

  Paired RNA sequencing data (21 runs/ 17 samples) of different tumors. The samples were prepared using the Illumina TruSeq stranded mRNA Kit. The sequencing was done on Illumina HiSeq 4000.

  Dataset EGAD00001009706

• Integrative Profiling of T790M Negative EGFR Mutated NSCLC Reveals Pervasive Lineage Transition and Therapeutic Opportunities

  We performed whole exome and transcriptome analysis of 59 first- and second-generation EGFR TKI resistant metastatic EGFR mutated patients to characterize and compare molecular alterations mediating resistance in T790M positive and negative disease. Transcriptomic analysis revealed ubiquitous loss of adenocarcinoma lineage gene expression in T790M negative tumors, orthogonally validated using multiplex immunohistochemistry. There was enrichment of genomic features such as TP53 alterations, 3q chromosomal amplifications, whole genome doubling and non-aging mutational signatures in T790M negative tumors. Almost half of resistant tumors were further classified as Immunehot, with clinical outcomes conditional on immune cell infiltration state and T790M status. Finally, using a Bayesian statistical approach, we explored how T790M negative and positive disease might be predicted using comprehensive genomic and transcriptomic profiles of treatment-naïve patients.

  Study EGAS00001005389

• Integrated Genomic and Transcriptomic Analysis of Small Cell Lung Cancer Reveals Inter- and Intratumoral Heterogeneity and a Novel Chemotherapy-Refractory Subtype

  We integrated histology, transcriptome, exome, and treatment outcomes of small cell neuroendocrine cancer (SCNC) from a range of metastatic sites, revealing complex intra- and intertumoral heterogeneity of neuroendocrine (NE) differentiation and transcriptomic subtypes (ASCL1, NEUROD1, POU2F3, YAP1 and ATOH1). High NE SCNCs were more likely to benefit from replication stress-targeted therapies, in contrast to non-NE tumors which were more likely to respond to immune response-targeted therapies.

  Study phs002541

• CRC cell line ChIP-seq

  ChIP-Seq data for CTCF, H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3 in C32, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines

  Dataset EGAD50000000295

• ICGC PCAWG Dataset: PACA-AU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: PACA-AU.

  Dataset EGAD00001003410

• ICGC PCAWG Dataset: PACA-AU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: PACA-AU.

  Dataset EGAD00001003411

• ICGC PCAWG Dataset: OV-AU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: OV-AU.

  Dataset EGAD00001003415

• ICGC PCAWG Dataset: OV-AU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: OV-AU.

  Dataset EGAD00001003416

• ICGC PCAWG Dataset: LICA-FR_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LICA-FR.

  Dataset EGAD00001002016