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• Leicester Mesothelioma Research Omics Dataset Committee

  This Data Access Committee consists of the mesothelioma research group led by Professor Dean Fennell.

  Dac EGAC50000000965

• Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden

  Profiling of circulating tumor DNA (ctDNA) may offer a non-invasive approach to monitor disease progression. Here, we developed a quantitative method, exploiting local tissue-specific cell-free DNA (cfDNA) degradation patterns, that accurately estimates ctDNA burden independent of genomic aberrations. Nucleosome-dependent cfDNA degradation at promoters and first exon-intron junctions was strongly associated with differential transcriptional activity in tumors and blood. A quantitative model, based on just 6 regulatory regions, could accurately predict ctDNA levels in colorectal cancer patients. Strikingly, a model restricted to blood-specific regulatory regions could predict ctDNA levels across both colorectal and breast cancer patients.

  Study EGAS00001004657

• Spatial transcriptomic data of HGSOC patients before and after treatment

  Spatial transcriptomic data of HGSOC patients before and after treatment

  Dataset EGAD50000000190

• PE-META-CENTRAL_ASIA-MATERNAL

  Fixed effect meta-analysis summary statistics combining GWAS of maternal preeclampsia cases and controls from Central Asia (Kazakhstan and Uzbekistan).

  Dataset EGAD00010001985

• Hepatitis C IL28B pooled resequencing study with 100 responders and 100 non-responders

  Hepatitis C IL28B pooled resequencing study with 100 responders and 100 non-responders

  Dataset EGAD00001000032

• HipSci - Bleeding and Platelet Disorders - Exome Sequencing - July 2017

  HipSci - Bleeding and Platelet Disorders - Exome Sequencing - July 2017

  Dataset EGAD00001003519

• HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017

  HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017

  Dataset EGAD00001003539

• ECA WES and RNAseq data

  40 samples of WES and their normal controls; 33 samples of RNAseq data.

  Dataset EGAD00001006740

• Gene Expression Analysis in Clonal Evolution of Fanconi Anemia

  We examined hematopoietic progenitor cells derived from iPSCs from patients with Fanconi anemia, including bone marrow failure cells (FANCA-/- HPCs), 'healthy', complemented cells (FANCA-/- cells with a wild-type FANCA cDNA), MDS-like cells (FANCA-/- HPCs with introduced mutations in RUNX1 and other MDS-associated genes), and Fanconi AML-like cells ('FAL'; MDS-like cells expressing FLT3-ITD).

  Study phs003024

• Subclonal variation in patients with pediatric T-lymphoblastic leukemia (T-ALL)

  Variations in TP53 and KRAS genes indicate a particularly poor prognosis in relapsed pediatric T-ALL. We hypothesized that these variations might be subclonally present at disease onset and contribute to relapse risk. To test this, we examined 386 children diagnosed with T-ALL, including more than 100 patients who relapsed as well as matched non-relapsing controls.

  Study EGAS50000000794

• PEVOsq WES data

  Raw paired FASTQ data of patients at baseline from the PEVOsq cohort

  Dataset EGAD50000001013

• preQC Genotypes

  preQC genotype data from the Affymetrix AxiomTM HGCoV2 1 array in plink ped/map format

  Dataset EGAD00010002437

• GLASS-NL DNA-Methylation

  DNA-methylation data of samples included in the GLASS-NL cohort

  Dataset EGAD00010002647

• EGA_PBC_phased

  A cohort of 2886 participants of the Japan PBC-GWAS Study

  Dataset EGAD00010001533

• BC WGS Dataset 3

  Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Dataset EGAD00001001351

• BC WGS Dataset 4

  Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Dataset EGAD00001001353

• University of Hull

  Tumour Regulatory Molecules in Early Pancreatic Cancer Detection (TEM-PAC) and EARLY DIAgnosis of PAncreatic Cancer by combined proteomics and genomics testing of pancreatic cyst fluid (DIA-PAC) studies.

  Dac EGAC50000000402

• Genomic and epigenomic sequencing data on human samples of Institut Curie.

  Total RNA sequencing, whole exome sequencing, whole genome sequencing and whole genome bisulfite sequencing on human samples collected at Institut Curie, France.

  Dac EGAC50000000356

• Multiple_myeloma_precursor_genomics

  Whole genome sequencing of up to 45 multiple myeloma precursor samples and matched normals pairs.

  Study EGAS00001006312

• Colorectal_organoids_and_tumour_tissue___Whole_Genome_X10

  Whole genome sequencing of single cell derived organoids from normal colon tissue and colorectal cancer.

  Study EGAS00001001100

• Point-of-care monitoring of head and neck cancer treatment response and recurrence development using nanopore-based ctDNA consensus sequencing

  Study EGAS00001007090

• Clear cell sarcoma sequencing data

  This study shares DNA and RNA sequencing data from Clear cell sarcoma patients

  Study EGAS00001006072

• ADAPTeR Study: WES data from ccRCC patients

  ADAPTeR study RNAseq from multi-region samples taken pre and post nivolumab.

  Study EGAS00001005638

• PE-META-CENTRAL_ASIA-FETAL

  Fixed effect meta-analysis summary statistics combining GWAS of fetal (baby) preeclampsia cases and controls from Central Asia (Kazakhstan and Uzbekistan).

  Dataset EGAD00010001987

• Copy Number Arrays

  Copy Number Alterations arrays from 21 patients and 24 samples performed by Affymetrix 6.0, Agilent 1M and Oncoscan CNV platforms

  Dataset EGAD00010001581

• 28 RNA-Seq from CAF-S1, CAF-S4 and EPCAM cells coming from Primary tumors and Lymph nodes of 5 patients)

  Dataset EGAD00001005744

• Cancer-associated genome-wide hypomethylation and copy number aberrations

  Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing

  Dataset EGAD00001001093

• CTCF-ChIP-Seq of cohesin-mutated and wildtype adult AMLs

  ChIP-Seq targeting CTCF in cohesin-mutated (STAG2 or RAD21 mutations) and wildtype adult AMLs (CTRL-AMLs).

  Dataset EGAD00001011200

• Single-cell CITE-seq and TCR-seq data from AIM⁺ HIV-1-specific T cells

  Single-cell sequencing data from 2 HIV-1 post-intervention controllers and 2 non-controllers reported in Fisher, Garcia, Frattari, Naasz, et al. Longitudinal samples were collected before antiretroviral therapy inititation, during suppressive therapy, and after analytical treatment interruption.

  Dataset EGAD50000002247

• Dataset Gene-Breakpoint Panel

  In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit.

  Dataset EGAD00001000365

• Hi-C in endometrial healthy and tumor tissues

  Hi-C libraries have been prepared by enzymatic digestion with MboI restriction enzyme and sonication. Illumina single-indexig primers have been use to amplify ligated fragments. Hi-C experiments have been performed on 10 slices (30um thick) of fresh-frozen tissues derived from 3 healthy and 3 tumor endometrial tissues of post-menopausal patients. Raw paired-end fastq.gz files are provided.

  Dataset EGAD00001010898

• Nanopore whole genome sequencing data of human PGT samples

  Data generated from embryo trophectoderm biopsies and corresponding parental blood samples

  Study EGAS50000000553

• UK10K COHORT IMPUTATION

  Imputation panel created from UK10K_COHORT_ALSPAC (EGAD00001000740) and UK10K_COHORT_TWINSUK (EGAD00001000741) datasets.

  Study EGAS00001000713

• Ulcerative colitis study - WES data

  Whole Exome Sequencing data of Single crypts, bulk crypt samples, and colitis-associated cancer.

  Study EGAS00001003801

• Parkinson's Families Project

  SNP array data of 698 individuals with early onset and/or familial Parkinson's disease.

  Study EGAS00001007906

• scRNAsequencing of in vitro expanded limbal stem cells of aniridia donors

  Identifying potential heterogeneity and expression differences within Aniridia limbal stem cells.

  Study EGAS00001007397

• Biomodal sequencing of normal blood and brain samples

  Whole-genome sequencing of normal blood and brain tissue using Biomodal multi-omics technology.

  Dataset EGAD50000001691

• PE-META-EUROPE-FETAL

  Fixed effect meta-analysis summary statistics combining GWAS of fetal (baby) preeclampsia cases and controls from Europe (UK, Iceland, Norway, and Denmark).

  Dataset EGAD00010001986

• PE-META-EUROPE-MATERNAL

  Fixed effect meta-analysis summary statistics combining GWAS of maternal preeclampsia cases and controls from Europe (UK, Iceland, Norway, Denmark and Finland).

  Dataset EGAD00010001984

• JAK and STAT alterations in CD30 positive LPD

  JAK and STAT alterations in CD30 positive LPD, panel sequencing, 12 cutaneous lymphoma patients, 40 samples

  Dataset EGAD00001005801

• Kinomics data

  To ellucidate protein activity in mRCC, Kinomics data was generated as part of the EuroTarget study

  Dataset EGAD50000002293

• Study2OrangeFiber

  SOMAscan plasma proteome datasets generated from participants consuming the orange fiber snack prototype (study 2)

  Dataset EGAD00010002191

• Study1PeaFiber

  SOMAscan plasma proteome datasets generated from participants consuming the pea fiber snack prototype (study 1)

  Dataset EGAD00010002192

• SolomonIslands.Dataset

  The tar archive contains unflitered genotype data from Pugach et al 2018 in plink format

  Dataset EGAD00010002306

• SEAsia.Oceania.Australia

  the tar archive contains unflitered genotype data from Reich et al AJHG 2011 study in plink format

  Dataset EGAD00010002302

• Present-day genomics from the Eurasian steppe

  502 genotypes obtained from Illumina DNA-arrays. Available as plink formatted files

  Dataset EGAD00010001538

• Bacteria Lateral sclerosis

  The study aims to find bacteria in neural tissue from patients with amyotrophic lateral sclerosis

  Dataset EGAD00001004458

• Belgian epilepsy patients

  The genomic sequence of brain expressed miRNA genes was sequenced in Belgian epilepsy patients.

  Dataset EGAD00001001851

• Swedish schizophrenia patients

  The genomic sequence of brain expressed miRNA genes was sequenced in Swedish schizophrenia patients

  Dataset EGAD00001001849

• Hessequa-descendants mitogenomes

  Complete sequence of the mitochondrial DNA of 87 Hessequa-descendant individuals

  Dataset EGAD00001007676

• ADARIO / Targeting ADAR1 in Immuno-Oncology

  RNA editing analyses of BRCA-isogenic cell lines and patient-derived xenografts (PDX)

  Study EGAS50000000518

• HCA_Immune_UAI_Paediatric_Spatial_Managed_Access

  Comparison of immune populations in adenoid tissue in patients with and without history of otitis media

  Study EGAS00001006471

• _RNAseq___Colorectal_organoids_and_tumoroids

  Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer

  Study EGAS00001000985

• Mutational_Analysis_of_Colorectal_PDX_models

  Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases.

  Study EGAS00001001171

• Nanopore whole genome sequencing data of HG002

  Data generated from single cell, 10 cells, and bulk samples of HG002.

  Study EGAS50000000552

• RNA-seq and WGS data of MB-0152

  Identification of fusion transcripts by RNA-sequencing and Whole genome sequencing of a breast cancer patient sample (METABRIC ID MB-0152)

  Dataset EGAD00001003342

• SYSCOL Human colorectal cancer project pilot RNA-seq and germline genotyping

  Genotyping by array and Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001000880

• BRAF and MEK resistant cell line clones

  BRAF and MEK resistant cell line clones

  Dataset EGAD00001000205

• (h)MeDIP-Seq of high-risk prostate cancer

  high-throughput sequencing of methylated and hydroxymethylated DNA from tumor and non-tumor tissue of patients with high-risk prostate cancer

  Dataset EGAD00001002010

• NanoString gene expression of PBMC from bladder cancer and RCC patients

  This dataset contains NanoString gene expression of PBMC from patients from IMvigor210, IMvigor211 and IMmotion150 cohorts

  Dataset EGAD00001005976

• Single Cell RNAseq of blood and tumor from renal cancer patients

  Single Cell RNAseq of blood and tumor from renal cancer patients

  Dataset EGAD00001005977

• RNA-Sequencing and Somatic Mutation Status of Adrenocortical Tumors: Novel Pathogenetic Insights

  RNA paired end sequencing of 59 adrenocortical tumors and 4 controls.

  Dataset EGAD00001006258

• Single cell sequencing of mild and critical COVID19 PBMC

  Single-cell RNA sequencing of 13 ‘mild-moderate’ and 10 ‘critical’ COVID19 PBMC samples

  Dataset EGAD00001006997

• Artificial mixtures of sonicated human and mouse DNA at different sizes were sequenced (PacBio)

  Artificial mixtures of sonicated human and mouse DNA at different sizes were sequenced

  Dataset EGAD00001008982

• Artificial mixtures of sonicated human and mouse DNA at different sizes were sequenced (Nanopore)

  Artificial mixtures of sonicated human and mouse DNA at different sizes were sequenced

  Dataset EGAD00001008981

• Chronic lymphocytic leukemia driven by paradoxical ERK activation during BRAF inhibitor treatment

  Whole-exome sequencing of a chronic lymphocytic leukemia (CLL) developed during vemurafenib treatment of a patient with malignant melanoma. Peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. DNA was extracted from highly purified (>97%) CD19+CD5+ cells obtained from the patient while being under BRAF inhibition versus CD14+ germline control cells (>90% purity). No alterations that could be linked to aberrant RAS activity or paradoxical RAF/MEK/ERK signaling could be identified in the CLL, which shows characteristic copy number alterations.

  Dataset EGAD00001000997

• Spatial transcriptome sequence data from HER2-positive human breast tumors (n=8, with 3 or 6 sections from each)

  Spatial transcriptome sequence data from HER2-positive human breast tumors obtained from the first generation of Spatial Transcriptomics arrays. The dataset contains 8 different tumors with 3 or 6 sections taken from each with paired-end sequencing.

  Dataset EGAD00001008031

• RNA-Seq - Characterization of a Breast Patient-derived Tumor Organoid biobank from an underserved population of patients

  RNA-seq datasets of patient and patient-derived organoids

  Study EGAS50000000683

• snRNAseq of ATCWGS42

  We performed single nucleus RNA-sequencing (snRNA-seq) on two regions from ATCWGS42 (ATCWGS42_E and ATCWGS42_R).

  Study EGAS50000001491

• Cell_lines_with_telomere_fusion_induced_rearrangements

  Whole-genome somatic rearrangement and point mutation analysis in cell lines with induced telomere fusions.

  Study EGAS00001001059

• Ulcerative colitis study - RNAseq data

  RNAseq data of rectal epithelial cells from Nfkbiz cKO and control mice after DSS administration.

  Study EGAS00001003802

• Patient data used in FLTseq paper

  Apply newly developed FLT-seq protocol and package FLAMES on a primary patient sample

  Study EGAS00001005597

• Genomic Study of Gastric Cancer

  We perform whole exome sequencing of 50 pairs of gastric cancer and matched normal samples

  Study EGAS00001005032

• nEODURVARIB clinical trial. Exome sequencing in advanced urothelial carcinoma

  Exome sequencing (BAM and VCF files) in advanced urothelial carcinoma in diagnostic and pos-ttreatment samples

  Dataset EGAD50000001162

• Nanopore whole-genome sequencing of human osteosarcomas

  We performed single and multi-region nanopore whole-genome sequencing on human osteosarcoma samples from adult and paediatric patients.

  Dataset EGAD50000000925

• TCR β-chain repertoire sequences of regulatory and conventional T cells in peripheral blood from breast cancer patients and healthy individuals

  Dataset EGAD00001004385

• Somatic mutation of SF3B1 in myelodysplasia with ring sideroblasts and other cancers

  Somatic mutation of SF3B1 in myelodysplasia with ring sideroblasts and other cancers

  Dataset EGAD00001000045

• RNA-seq data from sorted CML and normal samples

  RNA-seq data from sorted populations from 10 CML samples and 4 normal bone marrow samples.

  Dataset EGAD00001004079

• Targeted sequencing of head and neck squamous cell carcinomas

  This dataset includes 112 head and neck tumour samples with matched normal (blood) samples sequenced using a custom hybrid capture panel.

  Dataset EGAD00001004269

• BLUEPRINT Bisulfite-seq and Whole Genome Sequencing of mantle cell lymphoma

  BLUEPRINT Bisulfite-seq and Whole Genome Sequencing of mantle cell lymphoma

  Dataset EGAD00001001892

• Zhong Shan Hospital liver tumor single cell sequencing: 111 single cell and 6 tissues

  Zhong Shan Hospital liver tumor single cell sequencing: 111 single cell and 6 tissues

  Dataset EGAD00001002064

• Whole genome sequencing and genotyping of samples from CMBAN (Bantu from Cameroon)

  Whole genome sequencing and genotyping of samples from CMBAN (Bantu from Cameroon)

  Dataset EGAD00001005012

• Whole genome sequencing and genotyping of samples from CMSBA (Semibantu from Cameroon)

  Whole genome sequencing and genotyping of samples from CMSBA (Semibantu from Cameroon)

  Dataset EGAD00001005013

• Whole genome sequencing and genotyping of samples from TZWAS (Wasaamba from Tanzania)

  Whole genome sequencing and genotyping of samples from TZWAS (Wasaamba from Tanzania)

  Dataset EGAD00001005014

• Whole genome sequencing and genotyping of samples from TZCHA (Chagga from Tanzania)

  Whole genome sequencing and genotyping of samples from TZCHA (Chagga from Tanzania)

  Dataset EGAD00001005015

• Whole genome sequencing and genotyping of samples from TZPAR (Pare from Tanzania)

  Whole genome sequencing and genotyping of samples from TZPAR (Pare from Tanzania)

  Dataset EGAD00001005016

• Amplicon sequencing

  Fastq files from amplicon sequencing in 106 Multiple Sclerosis patients and 105 healthy volunteers in CD4 T cells, CD8 T cells and genomic DNA using PE300 Illumina MiSeq.

  Dataset EGAD00001005774

• NSCLC Whole Genome Sequencing data

  There are 64 NSCLC samples, including pre-treatment, post-treatment, and normal samples, sequenced by whole genome sequencing technology and archived in bam files.

  Dataset EGAD00001007977

• single cell sequencing esophagus, stomach and duodenum

  single cell sequencing esophagus, stomach and duodenum of : 4 esophagus samples 9 gastric samples 5 duodenum samples

  Dataset EGAD00001006417

• Whole transcriptome and whole exome sequencing of BPDCN patients

  Here, seven patients with BPDCN were characterized using RNA-seq and WXS.

  Dataset EGAD00001010314

• Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

  Study EGAS00001007402

• MiRNA_Validation

  Rounded Log2 CPM well-expressed miRNA levels in plasma; determined using the HTG EdgeSeq miRNA Whole Transcriptome Assay

  Dataset EGAD00010002752

• MiRNA_TrainTest

  Rounded Log2 CPM well-expressed miRNA levels in plasma; determined using the HTG EdgeSeq miRNA Whole Transcriptome Assay

  Dataset EGAD00010002754

• Baka_saliva_450K

  Epigenome of 36 rainforest hunther-gathering Baka of Cameroon by Illumina HumanMethylation450 array, used in the EGAS00001002226 study

  Dataset EGAD00010001251

• RNA Editing AZIN1 amplicon sequencing

  AZIN1 amplicon sequencing data of the EGAS00001000495 project.

  Dataset EGAD00001000708

• Tracing the origins of relapse in AML to stem cells

  Aligned whole genome sequence from AML relapse project

  Dataset EGAD00001003234

• AI_NF1glioma_WES

  The dataset includes 59 tumor samples from 56 NF1-glioma patients profiled by Whole Exome Sequencing.

  Dataset EGAD00001004375

• ICR MOPOPGEN UK exome control series

  BAM files of individuals from the 1958BC aligned to hg17

  Dataset EGAD00001004396

• Exome sequencing Parkinson's disease patients

  In this project we will sequence the exomes of 250 patients with Parkinson's disease

  Dataset EGAD00001000405

• IRF5 HL RNASeq dataset

  bam files associated with the study EGAS00001001205

  Dataset EGAD00001001417