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• EGA_PBC_phased

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

  Dataset EGAD00010001533

• EGAD00010000389

  Cambridge control samples using a 24k expression array from Illumina

  Dataset EGAD00010000389

• Determining the quality and complexity of NGS data without a reference genome

  Dataset EGAD00001000759

• Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms

  In this study, we aimed to comprehensively characterize in 113 myeloproliferative neoplasms (MPN) patients the mutational landscape of the granulocyte transcriptome using RNA sequencing data. We implemented workflows for fusion and variant calling, and differential splicing analysis for patients with hotspot SF3B1 mutations. Finally, we characterized the neoantigen landscape on individualized level taking each patient's HLA genotype (derived from the same RNA-seq dataset) into account.

  Study EGAS00001003486

• Saliba Lab Data Access Committee

  DAC for data generated by Saliba Lab at Helmholtz institute for RNA-based Infection Research, Würzburg, Germany

  Dac EGAC50000000152

• Screening for abnormal CGI methylation in primary colorectal tumours

  Screening for abnormal CGI methylation in primary colorectal tumours

  Dataset EGAD00001000213

• RNA-Seq data for Juvenile Pilocytic Astrocytomas

  RNA-Seq data for 9 JPA samples.

  Dataset EGAD00001009043

• Whole exome sequencing of ATCWGS42 primary tumour and PDX

  Genomic DNA was isolated from snap-frozen tissue and subjected to whole genome sequencing at The Center for Applied Genomics (Hospital for Sick Children, Toronto, ON) or at Beijing Genomic Institute (BGI). High-coverage whole exome-sequencing was performed at GeneSeeq Inc. (Toronto, Ontario, Canada) using IDT xGen exome panel.

  Study EGAS50000001490

• Whole exome sequencing of Parkinson's disease patients from the United Kingdom

  As part of the International Parkinson's Disease Genomics Consortium, exomes of Parkinson's disease (PD) patients and healthy controls were sequenced to study the genetic etiology of PD. This UK cohort consists of 70 PD patients. Researchers can apply for access to fastq, vcf and binary plink files for this cohort.

  Study EGAS00001002156

• RNA Sequencing of AD OM cells exposed to traffic-related air pollutants

  Total RNA sequencing of olfactory mucosa (OM) cells derived from individuals diagnosed with Alzheimer's disease exposed to traffic-related ultrafine particles (UFPs) for 24-h and 72-h in submerged cultures. The UFPs used for exposures were: A0, A20 and Euro6. Exposures were compared to the corresponding blank samples.

  Study EGAS50000000448

• Bulk 3' mRNA-Seq of dome and suspension tubuloids

  Bulk 3' mRNA-sequencing of human kidney tubuloids grown in dome and suspension culture for the identification of transcriptional differences associated with culture method, passage, and donor. Tubuloids were generated from 4 separate donors and collected for sequencing at day 7 of passage 3, 4, and 5 in dome and suspension culture.

  Study EGAS50000001629

• Single cell RNA sequencing of CD19 CAR T-cell infusion products

  We performed single cell RNA sequencing of remnants from CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma. Libraries were prepared using 10X 5’ GEX chemistry and sequenced on an Illumina HiSeq 4000 to obtain >50,000 reads per cell.

  Study EGAS00001004576

• WES for 45 patients with pleural mesothelioma (Matched)

  The dataset contains WES data (bam files) for 45 pleural mesothelioma samples. Nextera Flex for Enrichment solution (Illumina, San Diego, CA) in combination with SureSelect Human All Exon V7 probes (Agilent, Santa Clara, CA) was used for library preparation and generated libraries were sequenced on NovaSeq 6000 (Illumina, San Diego, CA) in 150 pair-end mode. Quality control of the raw data was conducted using fastQC (v. 0.11.8) (https://www.bioinformatics. babraham.ac.uk/projects/fastqc/). WES data were then analyzed with the DRAGEN Bio IT platform 49 (version 4.2.4) and the human GRCh38 as reference genome.

  Dataset EGAD50000002128

• WES for 42 patients with pleural mesothelioma (Not matched)

  The dataset contains WES data (bam files) for 42 pleural mesothelioma samples. Nextera Flex for Enrichment solution (Illumina, San Diego, CA) in combination with SureSelect Human All Exon V7 probes (Agilent, Santa Clara, CA) was used for library preparation and generated libraries were sequenced on NovaSeq 6000 (Illumina, San Diego, CA) in 150 pair-end mode. Quality control of the raw data was conducted using fastQC (v. 0.11.8) (https://www.bioinformatics. babraham.ac.uk/projects/fastqc/). WES data were then analyzed with the DRAGEN Bio IT platform 49 (version 4.2.4) and the human GRCh38 as reference genome.

  Dataset EGAD50000002127

• Dataset for whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors

  Dataset for whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors

  Dataset EGAD00001000810

• ChIP-seq and 4C-seq datasets in megakaryocytes and granulocytes from individuals with QPD and unaffected controls

  ChIP-seq was performed for the following histone modifications in both megakaryocytes and granulocytes: H3K27ac, H3K4me2, and H3K36me3. ChIP-seq was performed for H3K27me3 and CTCF in megakaryocytes only. All ChIP experiments consist of n=3 replicates for each of QPD and Control, with the exception of control granulocyte H3K4me2 for which only n=2 replicates were performed. 4C-seq datasets consist of 2 viewpoints (PLAU promoter and an intergenic enhancer), profiled in megakaryocytes from n=2 controls and n=4 QPD.

  Dataset EGAD00001006048

• Dataset for manuscript titled: Spatial Intra-Tumour Heterogeneity and Treatment-Induced Genomic Evolution in Oesophageal Adenocarcinoma: Implications for Prognosis and Therapy

  Dataset for manuscript titled: Spatial Intra-Tumour Heterogeneity and Treatment-Induced Genomic Evolution in Oesophageal Adenocarcinoma: Implications for Prognosis and Therapy

  Dataset EGAD00001015373

• NIH Division of Intramural Research Multiomic Monogenic Disease Study

  This cross-sectional, observational study utilized high-dimensional approaches, including transcriptomic analysis, serum protein profiling, and peripheral blood frequency assessments, to compare 228 adult and pediatric patients diagnosed with 22 monogenic immune-mediated conditions impacting various key immunological pathways, with 42 age- and sex-matched healthy controls. Participants were enrolled in clinical protocols at the National Institutes of Health in Bethesda, Maryland, USA. The primary objectives of the study were twofold: first, to identify disease-specific and shared "pan-disease" signatures using the collected data, and second, to develop a Random Forest classifier integrating these datasets to differentiate between age- and sex-matched healthy individuals and monogenic patients. This classifier produced a metric known as the "Immune Health Metric" (IHM). Subsequent analysis demonstrated that the IHM effectively distinguished healthy subjects from individuals with multiple polygenic autoimmune and inflammatory diseases in independent datasets. Moreover, it exhibited correlations with healthy aging and tracked disease activities and treatment responses across both immunological and non-immunological conditions. Additionally, the IHM accurately predicted age-dependent antibody responses to various vaccines, including influenza, Hepatitis A/B, Yellow Fever, Varicella Zoster, and Meningococcal vaccines.The microarray-based transcriptomic data, aptamer-based serum protein concentrations (Somalogic platform), peripheral blood frequency data, and clinical information will be made accessible through the database of Genotypes and Phenotypes (dbGaP).

  Study phs002732

• Asian Genome Project(BioBank Japan genotype data)

  Biobank Japan registrants sequenced for Asian Genome Project

  Study JGAS000647

• FFPE_Normal_Panel_V3_Cancer_Panel

  FFPE normal panel generation for use with V3 cancer panel 0618521

  Study EGAS00001000836

• Heart

  Whole-Exome-Sequencing of 5 pooled patients for SNP-based demultiplexing

  Study EGAS50000000655

• Identifying causative mutations for Thrombocytopenia with Absent Radii

  Identifying causative mutations for Thrombocytopenia with Absent Radii

  Dataset EGAD00001000018

• snv calls for subclonal reconstruction

  single nucleotide variant calls from somatic sniper, vcf format. input for subclonal reconstruction

  Dataset EGAD00001003753

• DATA FILES FOR SJLGG

  DATA FILES FOR SJLGG

  Dataset EGAD00001000695

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000854