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• CRUK Accelerator: Pancreatic neuroendocrine tumours (panNETs) whole exome and RNAseq raw sequencing data

  Whole exome and RNASeq raw sequencing data for an individual with multiple pancreatic neuroendocrine tumours (panNETs). Age at diagnosis was 51. Tumour tissue and PBMCs were used for sequencing. This data was generated as part of a study funded by a Cancer Research UK Centres Network Accelerator Award Grant (A21998).

  Dataset EGAD00001009685

• Whole genome sequencing data for five Japanese subjects

  WGS was performed for five Japanese subjects. DNA samples isolated from whole blood were sequenced at Macrogen Japan Corporation. All libraries were constructed using the TruSeq DNA PCR-Free Library Preparation Kit according to the manufacturer’s protocols. Libraries were sequenced on HiSeqX (Illumina, San Diego, CA, USA) or Novaseq6000 (Illumina, San Diego, CA, USA).

  Dataset EGAD00001010075

• A95662A

  Whole genome sequencing for single cells for library A95662A 637 samples; filetype=bam

  Dataset EGAD00001008226

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells, (ChIP-Seq_H3K27me3 for mature neutrophil, on genome GRCh37)

  ChIP-Seq_H3K27me3 data for 131 mature neutrophil sample(s). 321 run(s), 134 experiment(s), 134 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002712

• Whole genome sequencing of adult glioblastoma nuclei

  Three primary adult glioblastoma specimens were dissociated and nuclei were extracted. A portion of the nuclei was used for single-cell ATAC seq and the remainder were submitted for whole genome sequencing, to provide orthogonal validation of copy number variations in the samples compared to single-cell ATAC seq. Samples were sequenced on the Illumina NovaSeq 6000 in paired-end mode.

  Dataset EGAD00001007651

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells, (ChIP-Seq_H3K4me3 for mature neutrophil, on genome GRCh37)

  ChIP-Seq_H3K4me3 data for 133 mature neutrophil sample(s). 208 run(s), 136 experiment(s), 136 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002711

• BLUEPRINT release August 2014, Bisulfite-Seq for macrophage

  Bisulfite-Seq data for 1 macrophage sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000923

• BLUEPRINT release August 2014, RNA-Seq for common myeloid progenitor

  RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000907

• SCLC study MGH - RNAseq dataset

  RNA-seq analyses were performed on cDNA libraries prepared from PolyA+ RNA using the Illumina TruSeq protocol for mRNA. The final libraries were sequenced with a paired-end 2×75 bp protocol aiming at 8.5 Gb per sample for a 30x mean coverage of the annotated transcriptome. All sequencing reactions were conducted on an Illumina HiSeq instrument (Illumina, San Diego, CA, USA).

  Dataset EGAD00001003969

• BLUEPRINT release January 2015, RNA-Seq for common myeloid progenitor

  RNA-Seq data for 3 common myeloid progenitor sample(s). 3 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001169

• PROP1_study

  The dataset for the PROP1 study consists of samples of patients with combined pituitary hormone deficiency due to two most prevalent mutations in the PROP1 gene (c.301_302delGA and c.150delA) and healthy relatives and controls. All subjects were genotyped for 21 single nucleotide polymorphisms surrounding the PROP1 gene in order to assess the potential ancestral origin of the respective mutations. The genotype data are displayed in the vcf format.

  Dataset EGAD00001001303

• BLUEPRINT release January 2015, Bisulfite-Seq for erythroblast

  Bisulfite-Seq data for 2 erythroblast sample(s). 35 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 EGAD00001001133

• BLUEPRINT release August 2016, DNase-Hypersensitivity for CD4-positive, alpha-beta T cell, on genome GRCh38

  DNase-Hypersensitivity data for 1 CD4-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002480

• BLUEPRINT release August 2014, Bisulfite-Seq for erythroblast

  Bisulfite-Seq data for 1 erythroblast sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000909

• BLUEPRINT release January 2015, Bisulfite-Seq for macrophage

  Bisulfite-Seq data for 5 macrophage sample(s). 72 run(s), 5 experiment(s), 5 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 EGAD00001001192

• BLUEPRINT release August 2014, Bisulfite-Seq for inflammatory macrophage

  Bisulfite-Seq data for 3 inflammatory macrophage sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000914

• BLUEPRINT release January 2015, Bisulfite-Seq for inflammatory macrophage

  Bisulfite-Seq data for 3 inflammatory macrophage 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 EGAD00001001139

• BLUEPRINT release August 2016, DNase-Hypersensitivity for CD8-positive, alpha-beta T cell, on genome GRCh38

  DNase-Hypersensitivity data for 1 CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_dnaseseq_analysis_20160816

  Dataset EGAD00001002285

• BLUEPRINT release August 2015, DNase-Hypersensitivity for CD8-positive, alpha-beta T cell, on genome GRCh38

  DNase-Hypersensitivity data for 1 CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 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_dnaseseq_analysis_20150820

  Dataset EGAD00001001475

• Colorectal cancer WES/WGS analysis in Dr. Liu’s group in Sun Yat-sen University Cancer Center

  The samples include paired tumor and normal tissues from 205 patients (201 for normal and primary tumor tissues; 4 for normal, primary tumor and liver metastatic tissues). High-coverage WES sequencing or whole genome sequencing of DNA samples were performed on the Illumina HiSeq 2000 system

  Dataset EGAD00001003452

• The contribution of POT1 variants to sporadic melanoma development (2018-06-06)

  A case-control series of melanoma cases from Leeds, UK have been sequenced in the Fluidigm platform to identify genetic variants associated with sporadic melanoma development. Samples in which potentially contributing variants have been detected are being sequenced in an orthogonal platform for variant confirmation. . This dataset contains all the data available for this study on 2018-06-06.

  Dataset EGAD00001004151

• BLUEPRINT release August 2014, Bisulfite-Seq for Plasma cell

  Bisulfite-Seq data for 1 Plasma cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000927

• BLUEPRINT release January 2015, Bisulfite-Seq for plasma cell

  Bisulfite-Seq data for 1 plasma cell sample(s). 11 run(s), 1 experiment(s), 1 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 EGAD00001001160

• Transcriptomic Data for Manuscript with title: Comprehensive genomic profiling in esophageal adenocarcinoma unmasks potential precision therapies

  Transcriptomic Data for Manuscript with title: Comprehensive genomic profiling in esophageal adenocarcinoma unmasks potential precision therapies

  Dataset EGAD00001015476

• Metagenome for FINRISK2002

  The dataset contains data for n=7211 FINRISK 2002 participants who underwent fecal sampling. Demultiplexed shallow shotgun metagenomic sequences were quality filtered and adapter trimmed using Atropos (Didion et al., 2017), and human filtered using Bowtie2 (Langmead and Salzberg, 2012). The files are in FASTQ format.

  Dataset EGAD00001007035

• WXS dataset of Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

  WXS dataset of Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

  Dataset EGAD00001015638

• DNA Methylation Analysis of Prostate Cancer Cell Lines and Tissues Using Next Generation Sequencing

  Aberrant DNA methylation changes are known to occur during prostate cancer progression beginning with precursor lesions. Utilizing fifty nanograms of genomic DNA in Methylplex-Next Generation Sequencing (M-NGS) we mapped the global DNA methylation patterns in prostate tissues (n=17) and cells (n=2). Peaks were located from mapped reads obtained in each sequencing run using a Hidden Markov Model (HMM)-based algorithm previously used for Chip-Seq data analysis(http://www.sph.umich.edu/csg/qin/HPeak). The total methylation events in intergenic/intronic regions between benign adjacent and cancer tissues were comparable. Promoter CGI methylation gradually increased from -12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues and approximately 20% of all CpG islands (CGIs) (68,508) were methylated in tissues. We observed distinct patterns in promoter methylation around transcription start sites, where methylation occurred directly on the CGIs, flanking regions and on CGI sparse promoters. Among the 6,691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer specific and several previously studied targets were among them. A novel cancer specific DMR in WFDC2 promoter showed 77% methylation in cancer (17/22), 100% methylation in transformed prostate cell lines (6/6), none in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested a role for DNA methylation in alternate transcription start site utilization. While methylated promoters containing CGIs had mutually exclusive H3K4me3 modification, the histone mark was absent in CGI sparse promoters. Finally, we observed difference in methylation of LINE-1 elements between transcription factor ERG positive and negative cancers. The comprehensive methylome map presented here will further our understanding of epigenetic regulation of the prostate cancer genome. Overall Design: We mapped the global DNA methylation patterns in prostate tissues (n=17) and cells (n=2) from fifty nanograms of genomic DNA using Methylplex-Next Generation Sequencing (M-NGS). For replicate analysis in cell lines, a total of 4 runs were completed for PrEC prostate normal cell line, and 5 runs were completed for LNCaP prostate cancer cell line. For tissue samples, 2 benign prostate samples were sequenced twice on Illumina next generation sequencing platform to access overall repeatability of M-NGS.

  Study phs000597

• DAC for study Exon resequencing in patients with Brugada syndrome

  Dac EGAC00001000006

• DAC for the "Study on the proliferation history of colorectal adenomas"

  Dac EGAC00001000209

• DAC for study Population Structure and Genetic Diversity in Argentinean populations

  Dac EGAC00001000426

• DAC for genome-wide association study of prognosis in Crohn's disease

  Dac EGAC00001000568

• DAC for study Treg in breast cancer and healthy individuals

  Dac EGAC00001000638

• DAC for NKTL study. National Cancer Centre Singapore.

  Dac EGAC00001000640

• JKU and MUI Data Access Committee for targeted NGS panel data

  Dac EGAC00001000669

• DAC for the family-based genome-wide association study on CRSwNP

  Dac EGAC00001000742

• Data Access Committee (DAC) for NGS-based T-PLL data

  Dac EGAC00001000784

• Stanford Data Access Committee for Breast Cancer Tumor Heterogeneity through Treatment

  Dac EGAC00001000993

• Data Access Committee for Rare Coding Variants in Lupus Risk Genes

  Dac EGAC00001001157

• DAC for TCR-seq analysis of human intestinal Trm cells

  Dac EGAC00001001219

• DAC for Sex-biased patterns shaped the genetic history of Roma

  Dac EGAC00001001477

• Data Access Commitee for Translational Neurodegeneration Group - Technical University of Munich

  Dac EGAC00001001831

• Data Access Commitee for Translational Neurodegeneration Group Technical University of Munich

  Dac EGAC00001001916

• Data Access Committee for LUAD m6A profiling

  Dac EGAC00001002257

• University of Melbourne Centre for Cancer Research (UMCCR) Data Access Committee

  Dac EGAC00001002442

• EGAD00010000622

  SNP array data for gastric cancer cell lines

  Dataset EGAD00010000622

• DAC for "Integrated genetic analysis of primary CNS lymphoma"

  Dac EGAC00001003233

• Tapestri_h5

  H5 files generated for each sample with Tapestri Pipeline

  Dataset EGAD00010002559

• Tapestri_loom

  Loom files generated for each sample with Tapestri Pipeline

  Dataset EGAD00010002561

• DAC UMR Inserm U1236

  DAC for UMR Inserm U1236 laboratory

  Dac EGAC50000000217

• Institute of Pathology for Oncology Department at CHUV

  Prof Solange Peters

  Dac EGAC50000000008