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• Whole genome sequencing data from paired tumor and normal tissue in a cohort of NSCLC patients.

  WGS data for paired tumor and normal tissue from 260 patients in the TRACERx ctDNA study. The patient cohort is comprised of NSCLC patients undergoing surgical resection of their tumour. The patients were then followed up for a median of ~5 years after surgery, and serial blood samples were collected. The WGS data here was generated to inform the manufacture of custom ctDNA panels.

  Dataset EGAD50000001693

• Low-input RNA-seq libraries from FFPE samples using TaKaRa SMARTer kit

  Using the TaKaRa SMARTer Stranded Total RNA-Seq Kit v2, RNA-seq libraries were generated from 5 ng of RNA extracted from FFPE tissue. A low-input workflow was applied with 5 PCR cycles for the first amplification and 16 for the second. Library quality was assessed by Bioanalyzer and Qubit, and libraries were sequenced (2×150 bp) on the Illumina NextSeq 550 platform.

  Dataset EGAD50000001552

• RNA fastq files and mutation annotation files

  This dataset contains the results of both RNA sequencing and DNA sequencing. For RNA sequencing, it includes data from 12 samples derived from 9 patients, provided as raw sequencing files in FASTQ format. For DNA sequencing, it contains mutation information obtained from targeted panel DNA sequencing, including data from 35 individuals in the mutation annotation file (MAF) format.

  Dataset EGAD50000001768

• Emirati Phased Diploid Trio-Assemblies (27 Individuals, 54 Assemblies)

  This dataset comprises 27 phased diploid genome assemblies (i.e., 54 haplotypes) from Emirati family trios, provided in FASTA format. Sequencing used PacBio HiFi reads generated on the Revio platform at ≥25× coverage for each parent and offspring. Assemblies were produced with hifiasm (trio mode), then scaffolded with NTLink and reference-guided merging via RagTag against CHM13v2. The collection offers haplotype-resolved references suitable for downstream variant discovery and pangenome analyses.

  Dataset EGAD50000001755

• IMPRESS_all

  Dataset containing tumor, normal and blood sample data, for various tissue and tumor types. Data is targeted methylation data, using smMIP probes to target informative CpG sites in the genome. Sample type can be inferred from the name, with 'W' being normal samples and 'TC' tumor samples. Dataset contains 259 samples in duplicate, with one half of the runs being cut by MSRE's, and the other not. For every sample paired fastq files are present.

  Dataset EGAD50000000882

• scRNA-seq of Patient-derived tumor fragments (PDTFs)

  scRNA-seq of Patient-derived tumor fragments (PDTFs) which were treated with either Isotype (DP47), Isotype-IL2v (DP47-IL2v), anti-PD1 (PembroPGLALA) or PD1-IL2v (PembroPGLALA-IL2v) for 48 hours. Dataset content: 10 samples from 3 donors File type: paired-end fastq files Protocol: Chromium Single Cell 3' Reagent Kits User Guide (Dual Index) with Feature Barcoding technology for Cell Surface Protein (CG000317) Technology: Illumina sequencing Experimentation: scRNA-seq using the 10X technology

  Dataset EGAD50000000584

• paired-end FASTQ files from the study: Identification of the cause of juvenile parkinsonism in a case_SYNJ1

  The dataset consists of three samples: two controls and one case of juvenile Parkinsonism. Whole Exome Sequencing (WXS) was performed on these samples using hybrid selection for library preparation. Sequencing was carried out on the Illumina NextSeq 500 platform. For each sample, two FASTQ files containing paired-end reads (R1 and R2) were generated. The data deposited consists of the corresponding FASTQ files.

  Dataset EGAD50000000413

• scRNAseq and scTCRseq of three tumor lesions derived from one patient receiving adoptive TIL therapy

  scRNA sequencing and scTCR sequencing on three tumor lesions derived from one patient receiving adoptive tumor-infiltrating lymphocyte (TIL) therapy. Expanded metastasis was used for TIL expansion and yielded the TIL product which also was used for scTCR sequencing. 10 weeks after transfer of the TIL product the regressing metastasis was resected. After the patient progressed the progressing metastasis was removed (61 weeks).

  Dataset EGAD50000000406

• SNP array

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains SNP array data for tumor/normal pairs for a subset of 36 patients from the screening cohort plus an additional relapse tumor of one of those 36 patients. Data was generated on a OmniExpress-24 v1.1 Bead Array (Illumina) and is stored in IDAT file format.

  Dataset EGAD00010002597

• Quantitative analysis of a novel DNA hypermethylation panel using bronchial specimen for lung cancer diagnosis

  The dataset includes IDAT raw files for 10 samples and the analyzed DMP file which describes the differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. The histological type of the five lung cancer cases is adenocarcinoma and squamous cell carcinoma.

  Dataset EGAD00010002465

• Large deletion predisposes to familial melanoma

  Mutations in CDKN2A and CDK4 account for ~40% of multi-case melanoma families, with another ~10% attributable to BAP1 and genes associated with telomere maintenance. Thus, a substantial proportion of the genetic risk underlying familial melanoma remains unexplained.

  Study EGAS50000001496

• BGISEQ-500 Cancer Dataset - WGS tumour/normal pairs

  This study contains whole genome sequencing data for 3 matched tumour / normal pairs from Mesothelioma patients. The sequencing is 50bp paired-end generated using the BGISEQ-500 and is provided as 6 aligned and duplicate-marked BAM files.

  Study EGAS00001002298

• Evaluation_of_size_selection_on_cancer_specific_sequencing_libraries

  A couple of previously characterized and sequenced libraries will be repeated using a couple of differing size selection criteria and skim sequenced using an Illumina HiSeq. The resulting sequence will be analyzed to determine the optimal DNA library size for our specific downstream analysis.

  Study EGAS00001000293

• GWAS data (Illumina 2.5 M SNPs) in Cuban cohorts of dengue disease

  We will have 274 individuals typed for the Illumina Human Omni 2.5 chip. The individuals are from two locations in Cuba (Havana and Guantanamo) and from four phenotype classes (asymptomatic, control dengue fever and dengue hemorrhagic fever).

  Study EGAS00001002276

• Integrated genetic and epigenetic analysis of myxofibrosarcoma

  Myxofibrosarcoma (MFS) is a common histological subtype of adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high propensity for local recurrence. We underwent whole exome sequencing, RNA sequencing, and methylation analysis of MFS.

  Study EGAS00001002889

• Parallel Detections of Somatic Gene Mutations in Surgically Resected Tumor tissues and Matched Plasma Specimens in Early-Stages of Primary Breast Cancer

  We developed two panel successively, contain 68 and 136 genes respectively. Combination with ultrasound or mammography, it could be used for breast cancer early detection and avoided unnecessary surgery or other invasive detection.

  Study EGAS00001003075

• All available datasets of DEEP

  All available datasets of DEEP. There are several Reference Epigenomes available. For metadata check out www.deep.dkfz.de One reference epigenome represents a set of 6 ChIP-Seqs, WGBS, RNA-Seq, smallRNA-Seq and sometimes DNase1 and/or NOME-Seq.

  Study EGAS00001001608

• HCA_Heart_Disease_BHF_DZHK_RNA_

  Cell Atlas of the diseased human heart. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001004566

• Single cell RNA sequencing of lung adenocarcinoma.

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes.

  Study EGAS00001003681

• SPECTA__NGS_Screening_Program_for_Efficient_Clinical_Trial_Access

  SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer.

  Study EGAS00001000728

• Transcriptome_analysis_of_LCM_samples_

  We aim to set up a RNA pipeline for LCM samples to study transcriptome landscape of tumor and normal tissues. RNA was extracted from Lazer capture micro-dissection tissues and cDNA libraries were prepared with SMARTseq2 protocol. Libraries are pooled to be sequenced.

  Study EGAS00001003862

• STRATAA_RNAseq

  Transcriptome signatures of acute typhoid infection This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001003967

• Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma

  This dataset includes genomic information of 19 adult cerebellar glioblastomas (C-GBMs). Whole-exome sequencing data are available for 9 C-GBMs and their 8 corresponding matched blood samples, and glioma-specific targeted-DNA sequencing (GliomaSCAN) data from additional 10 C-GBMs are also available. Among them, Whole-transcriptome sequencing data were conducted for 6 C-GBM tumors.

  Dataset EGAD00001003417

• Evolution of four ER+ breast cancers

  The evolution of four breast cancers was analyzed using longitudinal samples collected over 2-15 years. Whole-genome sequencing and single-cell RNA-Seq were used to analyze evolution. We have deposited VCF files for SNV, indel, and structural variant calls from WGS data, and a text file showing transcripts per million (TPM) expression for the single-cell RNA-Seq data.

  Dataset EGAD00001003303

• GenomeDenmark Phase 2 - whole genome variants called using BayesTyper

  Variants and genotypes called in 50 danish parent-offspring trios from 80x Illumina sequencing data using BayesTyper. Data was produced using different insert size libraries of the sizes 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The sample IDs for the fathers and mothers are TrioID-01 and TrioID-02, respectively, and the IDs for the children are TrioID-0x, where x is a number between 3 and 7

  Dataset EGAD00001003188

• Exome sequencing data to study therapeutic targeting of ependymoma

  This dataset contains whole exome sequencing data from 24 patients. The Agilent SureSelect Human All Exon 50-Mb target enrichment kit was used to capture all human exons for deep sequencing. For each patient a tumour and control sample has been sequenced on a Illumina HiSeq2000 instrument in paired-end mode. Up to three lanes per sample have been sequenced resulting in 118 Fastq files.

  Dataset EGAD00001003973

• Fetal body map

  From 2nd trimester human foetuses we derived liver and intestinal stem cells. These were clonally expanded until enough material was available for whole genome sequencing. For each foetus, reference tissue (skin or bulk liver) was also sequenced to determine all germline variants. These were subtracted from the clones to determine all somatic mutations that had been acquired during embryonic and fetal development.

  Dataset EGAD00001003997

• Repeated clinical malaria episodes are associated with modification of the immune system in children. (2019-01-17)

  Repeated clinical malaria episodes are associated with modification of the immune system in children.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/. . This dataset contains all the data available for this study on 2019-01-17.

  Dataset EGAD00001004570

• Anaplastic Thyroid Cancer somatic variants (MuTect)

  Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls across the SureSelect All Exon V5+UTR target region. Somatic variant calls are in VCF format. In total there are 166 tumour samples, 94 of which have a matched normal. Somatic variants for tumours without a matched normal, were called against a panel of normals. Details for the mutect call can be found in the vcf header.

  Dataset EGAD00001004129

• Genotype calls (vcf files)

  Genotype calls for 83 Aboriginal Australian genomes split by chromosomes. In short, genotypes were called individually with samtools. They were subsequently filtered with thresholds related to sequencing depth, location of variants, sequencing error, and strand bias. Once combined, the genotypes were filtered when not in Hardy-Weinberg equilibrium. The genomes were phased with IMPUTE using the 1000 Genomes reference panel. NB: for the Y chromosomes​, only the 44 Aboriginal Australian males are included.

  Dataset EGAD00001004155

• Mutational_burden_in_skin_following_UV_treatment_Nanoseq

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007681

• Mutational_burden_in_skin_following_UV_treatment_WGS

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007682

• Mutational_burden_in_oesophagus__nanoseq_

  We wish to accurately assess mutational burden and signature from patients of different ages using clonal oesophageal epithelium and duplex-seq. We will also attempt to look for differences between smokers and non-smokers and individuals with different levels of alcohol consumption.

  Study EGAS00001007695

• Molecular profiling of DLBCL patients treated in the PETAL trial

  Using whole-exome sequencing and shallow whole genome sequencing for simultaneous screening of mutations, copy number alterations, and translocations, 5 biology-based risk profiles could be reproduced in an independent cohort of DLBCL patients, from the PETAL trial.

  Study EGAS00001005828

• Chromatin accessibility analysis of TFEB overexpression in LT-HSC

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentivirus overexpressing GP91 (CTRL) or TFEB. Six days later, BFP+ transduced cells were sorted for DNA extraction, library preparation and sequencing

  Study EGAS00001004971

• Exome_sequencing_of_UK_Birth_Cohorts___Avon_Longitudinal_Study_of_Parents_and_Children

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001005273

• RNA seq before and after cold pressor test

  The cold pressor test (CPT) is a widely used pain provocation test to investigate both pain tolerance and cardiovascular responses. Twenty-two females were phenotypically assessed before and after a CPT, and blood samples were taken for RNA-sequencing.

  Study EGAS00001006690

• Airway Dysbiosis Accelerates Lung Function Decline in Chronic Obstructive Pulmonary Disease

  This repository contains human sample derived microbiome full-length 16S rRNA sequencing data for sputum samples in COPD patients. The project goal is to understand the association of the lung microbiome with accelerated lung function decline in COPD patients.

  Study EGAS00001006444

• Transcriptomic analysis of MYC overexpression in LT-HSC.

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors (empty E CTRL or MYC). Six days after transduction, BFP+ transduced cells were sorted for RNA extraction and sequencing

  Study EGAS00001004970

• Exome_sequencing_of_UK_Birth_Cohorts___Born_in_Bradford

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001006978

• Exome_sequencing_of_UK_Birth_Cohorts___Millennium_Cohort_Study

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001007789

• 16S V3-V4 sequencing of lung microbiota from 17 NSCLC patients eligible for surgery without neoadjuvant treatment

  This dataset is composed of 86 samples: 15 samples of bronchoalveolar lavage fluid (BAL), 17 samples of non-malignant lung tissue, 14 samples of peritumoural tissue, 16 tumour tissues, 8 negative DNA extraction controls, 16 negative sampling controls for BAL. Samples were obtained from 17 NSCLC patients (average age 68 years). Sequenced region was 16S V3-V4. Fastq files are provided.

  Dataset EGAD00001006567

• BLUEPRINT release January 2015, Bisulfite-Seq for cytotoxic CD56-dim natural killer cell

  Bisulfite-Seq data for 3 cytotoxic CD56-dim natural killer cell sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001128

• BLUEPRINT release January 2015, Bisulfite-Seq for endothelial cell of umbilical vein (resting)

  Bisulfite-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001135

• BLUEPRINT release January 2015, ChIP-Seq for Acute promyelocytic leukemia

  ChIP-Seq data for 6 Acute promyelocytic leukemia sample(s). 25 run(s), 23 experiment(s), 23 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001138

• BLUEPRINT release January 2015, Bisulfite-Seq for CD4-positive, alpha-beta T cell

  Bisulfite-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 61 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001157

• BLUEPRINT release August 2015, Bisulfite-Seq for inflammatory macrophage, on genome GRCh38

  Bisulfite-Seq data for 6 inflammatory macrophage sample(s). 83 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001491

• BLUEPRINT release August 2015, RNA-Seq for megakaryocyte-erythroid progenitor cell, on genome GRCh38

  RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001492

• BLUEPRINT release August 2015, Bisulfite-Seq for conventional dendritic cell, on genome GRCh38

  Bisulfite-Seq data for 2 conventional dendritic cell sample(s). 30 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001497

• BLUEPRINT release August 2015, Bisulfite-Seq for alternatively activated macrophage, on genome GRCh38

  Bisulfite-Seq data for 5 alternatively activated macrophage sample(s). 79 run(s), 5 experiment(s), 5 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001498