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• ICGC PCAWG Dataset: MELA-AU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MELA-AU.

  Dataset EGAD00001002157

• Clonal fitness inferred from timeseries modeling of single cell cancer genomes

  Progress in defining genomic fitness landscapes in cancer by copy number alterations (CNA) has been impeded by lack of single cell and timeseries sampling. We generated 42,000 single cell whole genomes (scWGS) from breast epithelium and primary triple negative breast cancer (TNBC) patient-derived xenografts (PDX) collected during multi-year time series. Using a Wright-Fisher population genetics model, we inferred reproducible CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy, with accurate forecasting of experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDX resulted in cisplatin resistant clones that had shown low fitness in the untreated setting. By contrast high fitness clones from treatment naive controls were eradicated reflecting an inversion of the fitness landscape. Upon drug release selective pressure dynamics were reversed indicating a fitness cost of treatment resistance. Taken together, our findings reveal clonal fitness dynamics linked to CNA and therapeutic resistance in polyclonal tumours.

  Study EGAS00001004448

• Single-cell profiling maps the spectrum of crosstalk between glioma cells and tumor associated macrophages

  Tumor associated macrophages (TAMs) are a heterogeneous glioma infiltrate, implicated in cancer progression. We performed single-cell RNA-sequencing, to survey TAM response-patterns in glioma.

  Study EGAS00001002185

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set5)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of four hyperdiploid ALL patients (ALLT-502, ALLK-130, ALLK-137, ALLK-139). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq X Plus.

  Dataset EGAD50000002428

• Case Report: Pre-Clinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma

  We report a rare case of a young patient (VENUS 167) initially diagnosed with grade 1 endometrioid endometrial cancer, which, following endocrine treatment, presented with mixed aggressive carcinoma with three distinct histologic patterns: grade 1 endometrioid, large cell neuroendocrine, and undifferentiated carcinoma. The NGS fastq data are WES, RNAseq and ATAC

  Dataset EGAD50000002397

• Spatial CosMx Human 6K

  we profiled the cellular composition and TME spatial organization in 4 ICB-resistant HCC patients using single-cell spatial transcriptomics (CosMx Human 6K Discovery Panel). We identified 397 fields-of-view (0.51 mm by 0.51 mm) of hematoxylin and eosin (H&E)-defined tumor and stromal regions followed by cell segmentation using a nuclear stain plus 4 protein markers, yielding 485,209 high-confidence single-cell profiles that were subsequently categorized into distinct cell types based on marker gene annotation.

  Dataset EGAD50000002052

• WES_dataset1

  Fourteen MEITLs and one EATL previously had been sequenced using the SureSelectXT Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA).

  Dataset EGAD50000001620

• Human Single-Oocyte Transcriptome - Control and Cannabis Treated

  RNAseq data of human single oocytes exposed to THC and its metabolites, (mean concentration measured in the follicular fluid, THC1, n=95, 25 ng/mL Δ9-THC, 5 ng/mL 11-OH-THC, 50 ng/mL 11-COOH-THC) or a supraphysiologic, THC2, n=93, 100 ng/mL Δ9-THC, 50 ng/mL 11-OH-THC, 200 ng/mL 11-COOH-THC).

  Dataset EGAD50000001534

• RNA seq samples

  Dataset contains 12 RNA-Seq samples sequenced on the Illumina NextSeq500 sequencer. 6 samples are controls (D1-Tact-Plasma,D2-Tact-Plasma,D3-Tact-Plasma,D1-TUnstim-Plasma,D2-TUnstim-Plasma,D3-TUnstim-Plasma) 6 samples are case (D1-Tact-SF,D2-Tact-SF,D3-Tact-SF,D1-TUnstim-SF,D2-TUnstim-SF,D3-TUnstim-SF)

  Dataset EGAD50000001189

• ChIP seq samples

  Dataset contains 12 ChIP-Seq samples sequenced on the Illumina NextSeq500 sequencer. 3 samples are control samples (HcAct-Chip 1,HcAct-Chip 2,HcAct-Imput 2) 9 samples are case samples (HcAct2DG-Chip 1,HcAct2DG-Chip 2,HcAct2DG-Imput 1,JIAAct-Chip1,JIAAct-Chip2,JIAAct-Imput2,JIAAct2DG-Chip1,JIAAct2DG-Chip2,JIAAct2DG-Imput2)

  Dataset EGAD50000001188