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• Total RNA expression in benign ovarian and malignant ovarian tumours

  This study investigates the total RNA expression profiles of fresh-frozen ovarian tumors, providing a comprehensive analysis of 112 samples from 111 women in Sweden, two samples being replicates. The dataset includes 18 benign and 94 malignant tumours, collected as part of the U-CAN initiative from Uppsala Biobank. The sequencing data offers valuable insights into ovarian tumour biology and can be used to enhance understanding of tumour classification and molecular characteristics.

  Study EGAS50000001045

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001898

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001897

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001896

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001890

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001888

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001899

• Indonesian Microbiome Ecology and Evolution v1 (raw data)

  This dataset comprises 124 human faecal samples collected across Indonesia between 2015 and 2021, together with 6 controls. It was collected to study patterns of human microbiome variation across Indonesia’s diverse geography and lifestyles, and to generate the Indonesian Microbiome Ecology and Evolution (IndoMEE) metagenome-assembled genome (MAG) reference database. The dataset consists of 250 bp paired-end metagenomic reads from 124 faecal samples acquired from 116 individuals, at ca. 10.6 Gb / sample, together with 2 positive controls (ZymoBIOMICS Microbial Community DNA Standard by Zymo Research Cat# D6305), and 4 negative controls (for sampling: Blank, for extraction: Buffer EB by Qiagen Cat# 19086, for library prep: Nuclease Free Water by Ambion-Invitrogen Cat# AM9937). Library preparation was carried out using Illumina's TruSeq DNA Nano DNA kit, and sequencing was performed on the Illumina NovaSeq 6000 platform.

  Dataset EGAD50000001399

• Bulk RNA-sequencing data of advanced hepatocellular carcinoma (HCC) patients treated with atezolizumab plus bevacizumab.

  The dataset includes FASTq files and normalised gene expression counts from bulk RNA-sequencing of pre-treatment tumour (n=39) and adjacent non-tumour tissue samples (n=13) from advanced hepatocellular carcinoma (HCC) patients treated with atezolizumab plus bevacizumab. Specifically, RNA was extracted from the FFPE tumour tissue using RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA quality and quantity were evaluated using Agilent RNA 600 Pico Chips (Agilent Technologies). Sequencing libraries were prepared using the SMARTer Stranded Total RNA-seq kit v3 (Takara Bio). Sequencing was performed on an Illumina NovaSeq 6000 system. After obtaining the Fastq files, read 2 UMIs and adapters were trimmed using seqtk (v1.2), reads were aligned using STAR (v2.7.7a) to the human reference genome (GRCh38) and quantified with HTSeq (v2.0.2).

  Dataset EGAD50000001227

• MRC 60 snRNA-seq

  This dataset includes snRNA-seq generated from post-mortem brain and genotype from 60 individuals. The snRNA-seq data was generated using the 10X Single Cell Next GEM Chip targeting a minimum 5,000 nuclei per sample and libraries prepared using the Chromium Single Cell 3′ Library and Gel Bead v3 kit according to manufacturer’s instructions. cDNA libraries were sequenced using the Illumina NovaSeq 6000 system at a minimum sequencing depth of 30,000 paired-end reads per nucleus. Samples were pooled (max 4 per pool) and sequenced over 4 lanes. Pool-specific genotype files (containing genotype information at individual level) were used to demultiplex mapped pools into individual-level single-cell data. Donor DNA from samples processed at Imperial College were genotyped using the Illumina Infinium Global Screening Array v2.0.

  Dataset EGAD50000000965

• WES Breast Patient-derived Tumor Organoid

  This dataset includes 18 Whole Exome Sequencing (WES) samples from 5 subjects. WES is performed on a matched pair of case/control samples, e.g., tumor/control or organoid/control. For each patient, the same control sample is used for the analysis of tumor and organoid samples. The sample name structure identifies the type of sample: <subjectId>_[TON][12]_[Case|Ctrl]_EX2; where T, O, and N refer to Tumor tissue, Organoid, and control sample, respectively. The number 1 or 2 refers to the specific tissue, and Case and Ctrl indicate a tumor tissue (or organoid) and a control sample, respectively. For example, ICSBCS007_T1_Case_EX2 is the first tumor tissue of subject ICSBCS007; ICSBCS007_O1_Case_EX2 is the tumor organoid derived from that tumor sample, and ICSBCS007_N1_Ctrl_EX2 is the matching control sample. More information can be found in the sample information table.

  Dataset EGAD50000000961

• The epigenomic response of skeletal muscle in life-long high-level trained and untrained men and women after acute exercise

  To investigate the influence of lifelong exercise training on the response of skeletal muscle to a bout of acute exercise we generated targeted epigenomic data from long-term endurance (8 men) and strength (8 men) trained individuals and healthy age-matched untrained controls (8 men). Skeletal muscle biopsies were taken from M. vastus lateralis before, directly after, and 3hrs following acute exercise. Control subjects completed one bout of acute endurance exercise and one bout of acute resistance exercise, separated by 4-8 weeks, athletes completed one bout in their respective form of sports. All 96 samples were used for DNA extraction and targeted library construction using a custom Twist Biosciences panel and following EM-methylation tranformation were sequenced (2x150bp paired end) on the Illumina NovaSeq 6000.

  Dataset EGAD50000000512

• Single-cell RNA sequencing of pediatric Hodgkin Lymphoma to study the inhibition of T cell subtypes

  Here, we applied single-cell RNA-sequencing (scRNA-seq) on isolated HRS cells and the immune cells from the same pediatric classical Hodgkin Lymphoma (cHL) tumors. Specifically, 13 cHL patients and 3 reactive lymph node control samples were included in this cohort. This allowed us to identify genes of cell surface proteins that are consistently overexpressed in HRS cells and can potentially be used as targets for antibody-drug conjugates or CAR T cells. Finally, we identify potential interactions by which HRS cells inhibit T cells, among which the Galectin-1/CD69 and HLA-DRA/LAG3 interactions. However, high levels of inter-patient heterogeneity of the interaction strength were observed. In conclusion, this study identifies new potential therapeutic targets for cHL and highlights the importance of studying heterogeneity when identifying therapy targets.

  Dataset EGAD50000000626

• Alpha synucleinopathy spectrum - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA seq dataset from prefrontal cortex for a total of N=44 samples. Tissue samples correspond to patients with different alpha synucleinopathies. Specifically, idiopathic Parkinson's disease (PD, N=20) monogenic PD caused by LRRK2 mutations (LRRK2-PD, N=7), multiple system atrophy (MSA, N=6) and neurologically healthy controls (N=11). RNA seq was carried out using ribosomal depletion. The totality of these samples were also sequenced using single nucleus RNA seq, and available within the same study as a separate dataset.

  Dataset EGAD50000000430

• Complex-I stratification of Parkinson's disease - single nucleus RNAseq

  Single nucleus RNA seq dataset for CI stratification of Parkinson's disease Single nucleus RNA seq dataset of prefrontal cortex tissue from a total of N=18 samples. Tissue samples correspond to patients with idiopathic Parkison's disease (PD) with varying levels of Complex-I activity (N=12) and neurologically healthy controls (N=6). Single nucleus RNA seq was carried out using 10X Genomics Chromium. This dataset corresponds to a subset of the samples sequenced using conventional bulk tissue RNA seq and available within this Study as a separate Dataset.

  Dataset EGAD50000000432

• Complex-I stratification of Parkinson's disease in the prefrontal cortex - bulk RNA seq

  Dataset corresponding to the bulk RNA seq dataset from prefrontal cortex for a total of N=98 samples. Tissue samples correspond to patients with idiopathic Parkison's disease (PD) with varying levels of Complex-I activity (N=79) and neurologically healthy controls (N=19). RNA seq was carried out using ribosomal depletion. A subset of these samples was additionally sequenced using single nucleus RNA seq and is available in the same Study as an additional Dataset.

  Dataset EGAD50000000433

• Exome sequencing of early and late passage Patient Derived Xenogratf Tumoroids with matched Patient Derived Xenogratfs and matched normal liver

  The breadth and depth at which cancer models are interrogated contribute to successful translation of drug discovery efforts to the clinic. In colorectal cancer (CRC), model availability is limited by a dearth of large-scale collections of patient-derived xenografts (PDXs) and paired tumoroids from metastatic disease, the setting where experimental therapies are typically tested. XENTURION is a unique open-science resource that combines a platform of 129 PDX models and a sister platform of 129 matched PDX-derived tumoroids (PDXTs) from patients with metastatic CRC, with accompanying multidimensional molecular and therapeutic characterization. In this specific dataset we focused our attention on early (passage 3) and late (passage 8-12) PDXTs with their matched PDXs and normal liver

  Dataset EGAD50000000266

• ONGOING CHROMOSOMAL INSTABILITY ACROSS ANEUPLOID SUBTYPES OF CHILDHOOD B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA ASSOCIATES WITH DISEASE PROGRESSION

  Single-cells from primary cB-ALL samples were isolated using an inverted microscope coupled to a micromanipulator equipped with glass capillary for cell collection. A minimum of 20 cells were isolated per sample in microdrops of 2.5 μl of phosphate buffered saline (PBS) with 0.5% polyvinylpyrrolidone. Cell lysis and DNA amplification was performed using the SurePlex DNA Amplification System (Illumina). Genomic DNA was subsequently fragmented and tagged with the VeriSeq PGS transposome and the TruSeq Index adapters by PCR for library preparation (VeriSeq PGS Library Prep Kit, Illumina). Equal volumes of normalized libraries were pooled and sequenced on an Illumina MySeq platform with 1×75-bp single-end sequencing. Reads were subsequently aligned to the human reference genome (GRCh38/hg38) using Bowtie2 (version 2.2.4).

  Dataset EGAD50000000029

• Monotherapy Breast Cancer

  These samples are from locally advanced breast cancers that have been treated with epirubicin monotherapy before surgery. We will sequence some samples from patients with good response to the therapy and some with poor response to the therapy.

  Dataset EGAD00001000349

• Transcriptome Sequencing of Cancer Cell Lines

  In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Dataset EGAD00001000359

• RNA sequencing data of pediatric TCF3::PBX1 acute lymphoblastic leukemia

  TCF3::PBX1 leukemia is a rare subtype of B-cell acute lymphoblastic leukemia (B-ALL), occurring in approximately 3–5% of pediatric cases. It results from a chromosomal translocation t(1;19)(q23;p13), generating the TCF3::PBX1 fusion gene, which disrupts normal transcriptional regulation and contributes to leukemogenesis. Although historically associated with poor prognosis, contemporary risk stratification and intensified therapy have significantly improved outcomes, and both 5-years DFS and OS are nowadays ≥ 0.96.

  Study EGAS50000001797

• ecDNA copy number heterogeneity

  Neuroblastoma exhibits significant inter- and intra-tumour genetic heterogeneity and varying clinical outcomes. Here, we used DNA and RNA sequencing from the same single cells in cell lines and neuroblastoma patients to investigate these effects. We reveal extensive intercellular ecDNA copy number heterogeneity. We also provide direct evidence of how this heterogeneity influences the expression of cargo genes, including MYCN and its downstream targets, and the overall transcriptional state of neuroblastoma cells.

  Study EGAS50000000509

• Transcriptomic profiling of Hedgehog-high and Hedgehog-low HPV-negative HNSCC

  This study investigates transcriptomic differences between Hedgehog-high and Hedgehog-low HPV-negative head and neck squamous cell carcinoma (HNSCC). Tumors were stratified based on pathway-level genomic alteration scores and imaging-associated Hedgehog activity. RNA sequencing was performed on archival FFPE tumor samples to assess pathway activation and transcriptional programs associated with Hedgehog signaling. The dataset supports integrative radiogenomic and functional analyses of tumor-intrinsic signaling pathways.

  Study EGAS50000001549

• Development of actionable molecular targets and/or biomarkers for prognostication and patient stratification in gynecological cancer based on whole-exome sequencing and epigenomic analysis

  We collected 157 oral MPA-treatment samples from 66 cases (53 endometrial hyperplasia from 31 cases, 19 atypical polypoid adenomyoma from 14 cases, 1 normal endometrium from 1 case, and 84 endometrial carcinoma from 53 cases) and matched normal tissues/whole blood. The purpose of this study is to develop actionable molecular targets and/or biomarkers for prognostication and patient stratification.

  Study JGAS000813

• GCAT Hereditary Cancer Panel Sequencing Dataset

  This dataset comprises targeted sequencing data from 191 participants of the GCAT cohort generated using the I2HCP custom hereditary cancer panel. The panel is based on a custom bait library covering 122 genes associated with hereditary cancer syndromes, including genes related to hereditary colorectal cancer, hereditary breast and ovarian cancer, neurofibromatosis, and related disorders. Target enrichment was performed using a clinically validated design optimized for diagnostic accuracy. The panel and associated bioinformatic pipeline were previously validated, achieving analytical sensitivity and specificity greater than 99%. Sequencing data were processed using standardized alignment and variant calling procedures against the human reference genome. The dataset includes raw sequencing reads (FASTQ format) and processed variant call files (VCF format). All samples were pseudonymized prior to submission in accordance with ethical approvals and participant consent. Data are available under controlled access.

  Dataset EGAD50000002415