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• HGSC lines: ATACseq and RNAseq, pre- vs post-treatment with HKMTi-1-005

  Formation of a DAC to support the deposition of RNAseq and ATACseq data, from pre- vs post-treatment high-grade serous ovarian carcinoma cell lines. The lines include PEO1, PEO4, PEA2, OVCAR5, OVCAR8, and the treatment includes use of a novel epigenetic drug called HKMTi-1-005.

  Dac EGAC50000000034

• Unraveling the Physiological Impact of ANGPTL8 Loss-of-Function Variants in Humans

  Summary statistics and individual level data associated with PheWAS and phenotypic profiling of individuals with heterozygous loss of mutations in the gene ANGPTL8

  Study EGAS50000001482

• Whole-exome study to identify the causative germline mutations of congenital macrothrombocytopenia

  To identify the causative germline mutations of congenital macrothrombocytopenia, whole-exome study of 6 families (21 individuals) with autosomal dominant mode of transmission.

  Study EGAS00001000371

• Exome dataset of ALK study

  Here we sequenced biopsies from a patient with ALK-positive NSCLC progressing on first-line lorlatinib. This dataset contains one Exome-seq (the tumor and its normal). This aims to investigate the impact of the K1150dup mutation on lorlatinib progression and to explore potential therapeutic strategies to overcome resistance.

  Dataset EGAD50000002554

• Whole genome sequencing of C1498 cells.

  The dataset contains raw data (FASTQ) of whole genome sequencing of C1498 cells (n=1 sample). Libraries were prepared with the Illumina DNA PCR-Free Prep kit (Illumina, San Diego, CA, USA) and 150-bp paired-end reads were generated on the NovaSeq 6000 Sequencing System (Illumina).

  Dataset EGAD50000001826

• DCLRE1B/Apollo germline mutations associated with renal cell carcinoma impair telomere protection.

  We identified 2 germline mutations in the DCLRE1B gene encoding the Apollo protein by Whole Exome Sequencing (WES) in two families with inherited clear-cell Renal Cell Carcinoma. The raw data submitted here corresponds to WES performed on Genomic Platform at Gustave Roussy Institute.

  Dataset EGAD50000000311

• Exome sequencing analysis of BCP-LBL patients samples

  In order to perform comprehensive SNV and CNA analyses of a cohort of BCP-LBL patients, we performed whole exome sequencing of 41 tissue samples from BCP-LBL patients. Because the material was available as FFPE, the target coverage of the samples was >200x.

  Dataset EGAD50000000418

• The integrated genomic and immune landscapes of lethal metastatic breast cancer.

  We report on the extensive molecular profiling of multiple individual metastases from 10 warm autopsies of patients with lethal multi-therapy resistant breast cancers.

  Study EGAS00001002703

• Possible DNA Damage after paternal exposure to ionizing radiation in Radar technicians

  This dataset contains whole genome sequences from Illumina NovaSeq Devices sequenced at the WGGC Bonn to study effects of prolonged paternal exposure to ionizing radiation. Here we provide the reads, mapped to the hg19 reference genome of all samples.

  Dataset EGAD00001011043

• Spatial transcriptomics experiment

  This dataset include all spatial transcriptomics experiments. Samples coming from the same patient were sequenced on the same flowcell. Patients PTC4 to PTC9 were also sequenced on the same flowcell, as well as ATC1 and ATC2 on another one, and ATC3A and ATC3B on another one.

  Dataset EGAD00001011365

• WGS of 4 childhood T-ALL patients - tumor and remission

  Whole genome sequencing of 4 childhood T-ALL patients, which was further used in single-cell analysis in the paper "Single cell sequencing reveals the origin and the order of mutation acquisition in T-cell acute lymphoblastic leukemia".

  Dataset EGAD00001003951

• Maternal plasma data in FetalQuantSD accurate quantification of fetal DNA fraction by shallow-depth sequencing of maternal plasma DNA

  This dataset consist on 70 maternal plasma samples (bam files) used in the FetalQuantSD. The maternal plasma DNA samples were sequenced using the HiSeq 2000 platform (Illumina) with a 50-cycle paired-end mode.

  Dataset EGAD00001004324

• The polarity and specificity of antiviral T lymphocyte responses determine susceptibility to SARS-CoV-2 infection in cancer patients and healthy individuals.

  The goal of this study was to identify immune correlates of clinical protection against SARS-CoV-2 infection.

  Study EGAS00001005985

• Papuan Genomes: high depth (30x) whole genome sequence data

  This dataset includes the whole genomes, sequenced to high depth (30x) of 25 individuals from Papua New Guinea. The individuals were chosen from several geographically distinct Papuan groups, focusing on the highland regions: Bundi, Kundiawa, Mendi, Marawaka and Tari.

  Dataset EGAD00001001634

• Whole genome sequencing of matched esophageal tumor-normal samples

  The dataset includes whole genome sequencing (WGS) data on ten matched esophageal tumor-normal pairs. WGS was performed by the cancer sequencing service of CG with an average read coverage of approximately 50-fold. Illumina HiSeq2000 instrument was used to perform the sequencing.

  Dataset EGAD00001004832

• Paired-end RNA-seq analysis of the Hypermutation and Malignant Progression in Low-grade Glioma Patients

  44 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina RNAseq paired-end technology. Dataset contains 44 BAM files aligned to hg19 using Tophat 2.

  Dataset EGAD00001005387

• Dnase1l3 deletion causes aberrations in length and end-motif frequencies in plasma DNA

  We showed that mice in which Dnase1l3 had been deleted showed aberrations in the fragmentation of plasma DNA. We also observed a change in the ranked frequencies of end motifs of plasma DNA caused by the Dnase1l3 deletion.

  Dataset EGAD00001005071

• PBAT sequencing of naïve human ESCs

  This project investigates the DNA methylation landscape of naïve human embryonic stem cells (hESCs) derived from human embryos, assessing the impact of ERK inhibition (ERKi). Naïve ESCs were cultured in UXGL or PXGL media. Post bisulphite adaptor tagging protocol was used to profile genome-wide DNA methylation.

  Study EGAS50000001006

• Whole-exome sequencing (WES) analysis of untreated head and neck cancer patient-derived xenografts (PDXs) matched patient tumor tissue and normal mucosa tissue.

  WES analysis was performed on untreated patient tumor/normal mucosa tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC) to investigate the preservation of tumor-specific genomic alterations in the in vivo context.

  Study EGAS50000001622

• A single-cell atlas of meningioma.

  In this study, we examined the breadth of cell types and states in meningioma using the largest single-cell cohort of meningioma by generating more than 7.5 million total cells from meningioma and surrounding dura, profiled using single-nuclear RNA sequencing and high-resolution spatial transcriptomics.

  Study EGAS50000001589

• snRNA-seq of subcortical MS

  Single-nuclei RNA-sequencing (snRNA-seq) from subcortical white matter controls and MS lesions, specifically chronic active (CA) and chronic inactive (CI), that paired with the spatial transcriptomics from the same samples, was used to identify spatial niches and key cell interactions driving inflammation and disease progression.

  Study EGAS50000000354

• RNAseq data from 112 samples of benign or malignant ovarian tumours

  This dataset contains ~1.2 TB RNA sequencing data in fastq format from 112 samples of fresh-frozen ovarian tumours from a total of 111 women, two samples being replicates. The samples were collected from the U-CAN collection at Uppsala Biobank and include both benign (n = 18) and malignant (n = 94) tumours. The RNA sequencing samples were sequenced using paired-end sequencing (2x150 bp) on an Illumina NovaSeq 6000 instrument at the SciLifeLab National Genomics Infrastructure (NGI) in Uppsala.

  Dataset EGAD50000001521

• Phase II Trial with Correlative Genomic Analysis of Durvalumab plus Pazopanib Combination in Patients with Advanced Soft Tissue Sarcomas

  This study includes an open-label, phase 2 study to determine the activity of the anti-VEGF receptor tyrosine-kinase inhibitor, pazopanib, combined with the anti-PD-L1 immune checkpoint inhibitor, durvalumab, in unselected advanced sarcomas. We conducted whole exome and transcriptomic sequencing with pre-treatment tissue biopsy to correlate clinical outcomes with molecular and genomic biomarkers to identify patients who would most likely benefit from the combination treatment.

  Dataset EGAD50000000114

• RNA-Seq data from tumor samples collected from 12 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates differentially expressed genes associated with the progression of translocation renal cell carcinoma (tRCC) by analyzing RNA-Seq data from 23 tumor samples obtained from 12 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. RNA isolated from tumor samples was sequenced using the Illumina platform.

  Dataset EGAD50000000172

• MassArray1-80

  234 samples genotyped at 40 loci using the MassArrayiPLEX genotyping assay using the iPLEX Gold genotyping kit (Agena Biosciences, cat. 10148-2) Gabriel et al. (2009) [Gabriel, S. , Ziaugra, L. and Tabbaa, D. (2009), SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform. Current Protocols in Human Genetics, 60: 2.12.1-2.12.18. doi:10.1002/0471142905.hg0212s60]). Products were detected on a MassArray mass spectrophotometer and data were acquired in real time with MassArray RT software 4.0.0.2 (Agena Biosciences). SNP clustering and validation was carried out with Typer 4.0.26.75 software (Agena Biosciences).

  Dataset EGAD00010001906