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• Whole-genome and single-cell sequencing of lethal metastatic castration resistant prostate cancer

  Contains a total of 9 patients with whole-genome sequencing of 30 tumours or germline samples, 10X single-cell multiome RNA-seq + ATAC-seq of 24 tumours, 10X 5' single-cell RNA-seq of 10 tumours, and snPATHO-seq of 2 primary tumours. All single-cell experiments have matched whole-genome sequencing. When matched tumour (and germline) whole-genome sequencing is missing, it can be found under EGAS00001006598.

  Dataset EGAD50000001869

• TenK10K Phase 1: Whole Genome Sequencing SNP + indels multi-sample VCFs

  SNP and indel variants were called for 1,925 samples from phase 1 of the TenK10K project. Variant calling from WGS alignments to the GRCh38 reference assembly was performed using GATK4 HaplotypeCaller in DRAGEN mode. These VCFs consist of common (>=1% minor allele frequency [MAF]) and rare (<1% MAF) variants . This dataset is comprised of autosomal variants provided as multisample compressed VCF format files. Principal component scores were derived by using gnomAD’s run_pca_with_relateds method.

  Dataset EGAD50000002377

• De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

  Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic (RNA-seq) and epigenetic (ChIP-seq) hallmarks of EwS.

  Dataset EGAD50000001673

• Tumor Profiler Project - OV scDNA data additional samples

  The dataset contains 10x Chromium single-cell DNA sequencing data from 6 samples from 5 different patients with ovarian cancer. 4 samples were collected from the tumor, and 2 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. This dataset contains additional samples from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001294

• Tumor Profiler Project - OV scRNA data additional samples

  The dataset contains 10x Chromium single-cell transcriptomics data from 6 samples from 4 different patients with ovarian cancer. 3 samples were collected from the tumor, 3 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. This dataset contains additional samples from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001293

• RnaSeq data from 414 tumor samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 414 BAM files corresponding to the full total RNA-sequencing dataset.

  Dataset EGAD50000000733

• WES data from study: Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma

  The ChRCC study WES dataset contains raw whole exome sequencing data of 17 tumor and 7 adjacent normal samples from 7 UTSW patients, who have consented to depositing their genomic data to public repository. WES was performed using 75bp paired-end fragments at an average read depth > 100x on a HiSeq2500 platform (Illumina, San Diego, CA, USA). The raw data is in fastq format.

  Dataset EGAD50000000415

• Evaluating potential drug candidates for the treament of Henamgiopericytoma on patient derived cell line models

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1. Potential drug candidates that could be repurposed for the treatment of SFT/HPC were screened. Screening was performed through RNA-Seq

  Dataset EGAD50000000039

• Genomic Signatures Reveal DNA Damage Response Deficiency in Brain Metastases of Colorectal Cancer

  Brain metastasis (BM) of colorectal cancer (CRC) is rare but lethal and lacks effective therapies or a good understanding of its genomic landscapes. We conduct an analysis of whole-exome sequencing (WES, Illumina HiSeq 2500 sequencing platform) on 11 patient-matched BMs, primary CRC tumours, and adjacent normal tissues; and whole-genome sequencing (WGS, Illumina HiSeq X Ten platform) on 8 patient-matched BMs, primary CRC tumors, and adjacent normal tissues to uncover the whole-genome mutational landscape of colorectal cancer with brain metastasis.

  Dataset EGAD00001005030

• The effect of anti-HER2/CD3 TDB on transcription in human CD8 T cells (bulk RNA-seq)

  RNA was isolated from purified human CD8 cells that were incubated with anti-HER2/CD3 TDB in the presence of SK-BR-3 cells. Sequencing libraries were generated and submitted for transcriptome profiling by high-throughput sequencing. Experiments were performed in triplicates for anti-HER2/CD3 TDB treatment and control. This Dataset is associated with the following ArrayExpress Experiment: E-MTAB-8211 - The effect of anti-HER2/CD3 TDB on transcription in human CD8 T cells (bulk)

  Dataset EGAD00001005187