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• Multi-omics datasets (WES, RNA-seq) of mesothelioma MIST4 study, a phase II PD-L1/VEGF blockage clinical trial

  This study comprises 26 mesothelioma patients with whole exome and RNA sequencing, designed to examine the efficacy and correlates of response to dual inhibition of programmed death-ligand 1 and vascular endothelial growth factor inhibition.

  Study EGAS50000001818

• Immunoprotective mechanisms and microbiota interplay in Salmonella Typhi infection

  Vaccine development against Salmonella enterica serovar Typhi (S. Typhi) requires a better understanding of interaction between human host and the resident microbial consortia in gastrointestinal tract. Healthy adult volunteers received either Ty21a, M01ZH09 or placebo, and underwent challenges with wt S. Typhi. Stool samples were collected at the screening interview (Baseline 1), prior to the first vaccination visit (Baseline 2), during vaccination (Day -28 and -26 for placebo and M01ZH09 groups; Day -32, -30, -28, -26 for Ty21a group), prior to challenge with S. Typhi (Day 0), and after challenge (day 0 12h, day 1, day 3, day 7, and day 10). 16S rRNA and messenger RNA were extracted from stool and sequenced on the Illumina Miseq and HiSeq 2000 platforms, respectively.

  Study phs001521

• Diseased_heart_analysis__RNA_Adult

  Samples for this project are taken from adult human hearts which have been preserved using 2 different methods (cold static storage on ice, and hypothermic perfusion). Samples have been acquired at various time points during post-preservation normothermic perfusion. The aim of the project is to assess the transcriptional changes caused by these differing methods of preservation.

  Study EGAS00001008302

• Short read sequencing dataset of pathogen-stimulated PBMCs

  QuantSeq 3'-mRNAseq. 5 donors, 4 stimuli, 2 time points

  Dataset EGAD50000000012

• Methylation_PBL_IBD_LTS

  Longitudinal whole-genome DNA methylation profiling of PBL obtained from IBD patients (CD and UC) at two different time points

  Dataset EGAD00010002402

• UK Biobank whole cohort directly genotyped and imputed data (~500,000 participants)

  Genotype data is available for all 500,000 participants in the UK Biobank cohort. Genotyping has been performed using the Affymetrix UK BiLEVE Axiom array on an initial 50,000 participants and the remaining 450,000 participants have been genotyped using the Affymetrix UK Biobank Axiom® array. The two arrays are extremely similar (with over 95% common content).Quality control and imputation (to over 90 million SNPs, indels and large structural variants) has been performed by a collaborative group headed by the Wellcome Trust Centre for Human Genetics.The following data are available:* A clean set of QC’ed genotype calls* Confidence values that a genotype call is correct* Intensity data to generate cluster plots* Extensive QC information regarding SNPs and samples including SNP metrics, batch effects, population structure and relatedness* Imputed dataFor further information, please refer to the UK Biobank website

  Study EGAS00001002399

• Beacon v2

  Beacon v2: a tool for data discovery Motivation In the era of data-driven health research and personalised medicine, human genomic data has become extremely valuable. These are also identifiable data, as they carry information pointing to a specific individual as well as their own family; and as such, they must be protected. This makes data discovery particularly challenging: this is where "Beacon" comes in. A "Beacon" is an API aiming to enable the search of genomic variants and associated information without jeopardising the privacy of the dataset. Here, we refer to its current version, namely version 2 (v2). Definition Beacon v2 is a term that can refer to different aspects. The EGA is playing a central role in the following aspects: The Beacon v2 protocol is a Global Alliance for Health and Genomics standard. The Beacon v2 Reference Implementation (B2RI) is an "out-of-the-box" Beacon instance developed with ELIXIR, which facilitates Beacon deployment. The EGA Beacon(s) are Beacons following the v2 standard and using the B2RI, deployed on top of data hosted at the EGA and allowing for their discovery. Resources Depending on whether you are visiting us a stakeholder (you need more general information about Beacon), a deployer /implementer (you want to have your own Beacon instance), or an EGA user (you want to query Beacon and start browsing data), you will be interested in the following resources: Your role Beacon aspect Documentation type Stakeholder Beacon v2 protocol Beacon website Beacon page on the GA4GH website Deployer/Implementer Beacon v2 protocol Read the docs: Beacon v2 standard technical description GitHub repository Beacon v2 standard Beacon v2 Reference Implementation Read the docs: B2RI technical description GitHub repository B2RI Guide to deploy Beacon using B2RI EGA user EGA Beacon EGA AF Browser

  Documentation about/projects-and-funders/beacon

• Metastatic Prostate Follow Up 2

  Validation/deeper sequencing for metastatic prostate cancer samples

  Dataset EGAD00001000989

• R compatible Seurat's objetc .rds files with count data and metadata from single cell RNA seq analysis to characterize the prostate cancer tumoral microenviroment of 31 fusion biopses.

  Pre-processed Seurat objects with cellular and functional annotation information from the scRNAseq study on PC fusion biopsy samples. The data consists of rds files composed of normalised counts matrices, normalised and scaled counts, functional enrichment counts at the cellular level and metadata with patient grouping and cellular annotation variables. There are 3 .rds files, one with the total cells (SCP_data_analysis), with the selection of cells annotated as cancerous (selected_cancer_analysis) and cancer-associated fibroblasts (selected_caf_analysis).

  Dataset EGAD50000001298

• WES of melanoma tumors treated with combined immune checkpoint blockade

  This study of pre-treatment melanoma tumor samples from patients subsequently treated with combined anti-CTLA-4 and anti-PD-1 checkpoint blockade sought to identify genomic biomarkers of response to therapy. A total of 26 tumor and matched normal samples underwent whole exome sequencing.

  Study EGAS00001003857

• Comparison of 3 protocols for deriving pancreatic progenitors from hPSCs (RNA-seq)

  This dataset contains 26 mapped bam files. The samples were generated with 3 different protocols for deriving pancreatic progenitors from hPSC. Three parallel differentiations were performed, all done in a hPSC NKX6.1-GFP reporter line. For each protocol there are three cellular populations: total (presort), GFP+ and GFP- . In summary: 3 differentiations x 3 protocols x 3 cellular populations. We prepared Smart-Seq2 RNA-seq libraries for the 27 samples, 1 sample failed library preparation and is not therefore included in this dataset.

  Dataset EGAD00001004823

• MutWP1: CRUK Grand Challenge Mutographs of Cancer: kidney (2019-03-26)

  This dataset contains all the data available for this study on 2019-03-26.

  Dataset EGAD00001004867

• Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.

  This dataset consists of shallow whole genome sequencing data and amplicon sequencing data for 26 ovarian cancer patients (21 high-grade serous ovarian cancer, 4 low-grade serous ovarian cancer and 1 clear cell ovarian cancer). The data are provided as single end FASTQ files for the shallow whole genome sequencing data (31 libraries) and paired end FASTQ files for the amplicon sequencing data (98 libraries).

  Dataset EGAD00001008716

• Single nucleus RNA Seq of LUAD patient derived lung samples

  Fastq files of single nucleus RNA Sequencing data from 26 patients including 26 lung adenocarcioma and 12 matched healthy tissue samples for 8 young female never smokers, 8 young female smokers, 7 elderly female never smokers and 3 male never smokers.

  Dataset EGAD00001008955

• Average_5mC_Roadmap_histoneMarks

  Average methylation levels based on nanopolish calls from Roadmap Epigenomics histone mark annotations using different cell types. Data from 8 individuals at different time points.

  Dataset EGAD00010002422

• Average_5hmC_Roadmap_histoneMarks

  Average hydroxymethylation levels based on megalodon calls from Roadmap Epigenomics histone mark annotations using different cell types. Data from 8 individuals at different time points.

  Dataset EGAD00010002417

• Average_5hmC_Roadmap_chromatinStates

  Average hydroxymethylation levels based on megalodon calls from Roadmap Epigenomics chromatin state annotations using different cell types. Data from 8 individuals at different time points.

  Dataset EGAD00010002414

• Average_5mC_Roadmap_chromatinStates

  Average methylation levels based on nanopolish calls from Roadmap Epigenomics chromatin state annotations using different cell types. Data from 8 individuals at different time points.

  Dataset EGAD00010002413

• CPC-GENE Prostate Cancer Heterogeneity Study

  Raw sequence data, fastq format

  Dataset EGAD00001002885

• Lindsey E. Jones et al. Patient-derived cells from recurrent tumors that model the evolution of IDH-mutant glioma. Neuro-Oncology Advances, 2020. We established robust, versatile, and well-characterized Patient Derived Cells (PDC) of an IDH1-mutant astrocytoma and an IDH1-mutant oligodendroglioma that represents defined evolutionary stages of chemotherapy-induced hypermutation. The PDCs retain tumor subtype defining features over time as well as classic hallmarks of cancer, including anchorage independent growth and cell immortality. The integrated phylogenies composed of PDCs,single-cell-derived PDCs, patient-derived xenografts, and corresponding spatiotemporal tumor tissue samples also provide new insight into the clonality, evolutionary pattern, and immense mutational load of hypermutated IDH mutant gliomas.

  IDH-mutant lower-grade gliomas can undergo malignant progression via temozolomide-driven hypermutation. Patient-derived cells (PDC) that model the genetically distinct hypermutated (HM) tumor subgroup are generally lacking, and few if any human brain tumor cell models are from defined evolutionary time points. Here, we characterize multiple PDC derived from independent surgical specimens of IDH1-mutant recurrences, including an ATRX and TP53-mutant astrocytoma and a 1p/19q co-deleted and TERT promoter-mutant oligodendroglioma. We determined the evolutionary time points represented by each PDC using exome sequencing and phylogenetic reconstruction, comparing the PDC and single cell clones of the PDC (scPDC) to multiple spatiotemporal tumor tissue samples, PDC-derived xenografts (PDX) and patient-matched blood. The tumor samples exhibited TMZ-induced mutagenesis and a branching pattern of evolution. We found clear evidence of two fully independent founder HM clones in the tumor tissue that are faithfully represented by independent PDC. The PDC, scPDC and PDX also shared the mutagenesis signature and represent the mid and later evolutionary time points of their corresponding tumors. The PDC maintained the tumor subtype-defining features over many passages, including heterozygosity of the IDH1 R132H mutation, production of 2-hydroxyglutarate (2-HG), and subtype-specific telomere maintenance mechanisms. The PDC from both tumors exhibited anchorage-independent growth in soft agar. The oligodendroglioma PDC formed infiltrative intracranial tumors with characteristic oligodendroglioma histology, initially with a long period to tumor formation. We conclude that the PDC, scPDC and PDX faithfully model the heterogeneous clonal origins of the corresponding tumor tissue. The multilevel analysis also provides new insight into the intratumoral heterogeneity and vast mutational load of HM glioma. The PDC from multiple evolutionary time points presented in the context of full clinical timelines may be useful to model evolution and intratumoral heterogeneity, important sources of therapeutic failure.

  Study EGAS00001003992

• Average_5hmC_TF_sites

  Average hydroxymethylation levels on transcription factor binding sites obtained from ENCODE (ChIP-sequencing of GM12878 lymphoblastoid cell line). Data from 6 individuals at different time points.

  Dataset EGAD00010002421

• Functional characterisation of CpG islands in human tissues

  Functional characterisation of CpG islands in human tissues

  Dataset EGAD00001000212

• RNAseq SCLC Cell lines MYC

  RNAseq data set (Mollaoglu et al., MYC drives progression of small cell lung cancer to a variant neuroendocrine subtype with vulnerability to Aurora kinase inhibition) RNA isolation from primary tumors and healthy lungs was performed using RNeasy Mini Kit (Qiagen) with the standard protocol. RNA was subjected to library construction with the Illumina TruSeq Stranded mRNA Sample Preparation Kit (cat# RS-122-2101, RS-122-2102) according to manufacturer’s protocol. Chemically denatured sequencing libraries (25 pM) are applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001). Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).

  Dataset EGAD00001003099

• Genetic_vulnerability_of_knockout_cancer_lines

  Genome-wide CRISPR/Cas9 library screen was performed in isogenic cell lines. Three biological replicates were used. Cells were harvested at initiation of screen and at specific time points following cell culture. Using this approach we aim to identify genes specifically important in cell survival in engineered cell lines. Please perform 72, instead of 36, PCR reactions as the screen performed at 200x coverage.

  Study EGAS00001002253

• Error-corrected sequencing of 26 driver genes

  387 swab samples were sequenced. The bam files contain consensus reads.

  Dataset EGAD50000000079