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• The life-saving benefit of dexamethasone in severe COVID-19 is linked to a reversal of monocyte dysregulation

  Assessment of dexamethasone response in human lung through scRNA-seq analysis of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19.

  Study EGAS50000000203

• Whole-exome sequencing data of patients with T follicular helper cell lymphomas

  This dataset contains WES data analyzed using the Genomon2 pipeline (v.2.6.2, https://github.com/Genomon-Project) from 14 patients with T follicular helper cell lymphomas (TFHLs). A list of somatic mutations called by the Genomon2 pipeline for each sample is provided as a txt file.

  Dataset EGAD50000000401

• Tumor Profiler Project - AML scRNA data

  The dataset contains single-cell RNA seq data from 23 patients with Acute Myeloid Leukemia (AML). Samples were collected from bone marrow or blood. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000000823

• Pregnancy-associated melanoma

  The aim of this project is to assess differences in intratumoral immune composition in pregnant melanoma patients versus non pregnant melanoma controls. Samples (N=25) were obtained from a local patient database. From archived FFPE we isolated RNA and performed NGS and bio-informatica data-analysis.

  Dataset EGAD50000000706

• Tumor Profiler Project - MEL scRNA data

  The dataset contains 10x Chromium single-cell transcriptomics data from 65 samples from 62 different patients with melanoma. Samples were collected from the tumor. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000000853

• Genomic characterization of CNA-quiet oral cancer

  Low-coverage whole genome sequencing and targeted (30 gene panel) deep sequencing of oral cancer. Note that the targeted deep sequencing is not actually amplicon sequencing but hybrid capture sequencing, which was not available as on option.

  Dataset EGAD50000000790

• Single cell and spatial transcriptomics of adult human adrenal glands

  The data set is composed of single cell transcriptomics data for adrenal glands from 11 deceased organ donors (10x 3') and spatial transcriptomic data for adrenal glands from 4 deceased organ donors (10x Visium).

  Dataset EGAD50000000394

• RNA-sequencing of PBMCs from COVID-19 patients experiencing different degrees of the disease (mild and critical), and control patients

  Bulk RNA-sequencing of peripheral blood mononuclear cells collected from mild COVID-19 (n = 4), critical COVID-19 (n = 12) and control (n = 8) patients. Sequencing data is provided as FASTQ files.

  Dataset EGAD50000001405

• miRNA-sequencing of PBMCs from COVID-19 patients experiencing different degrees of the disease (mild and critical), and control patients

  micro RNA-sequencing of peripheral blood mononuclear cells collected from mild COVID-19 (n = 6), critical COVID-19 (n = 13) and control (n = 8) patients. Sequencing data is provided as FASTQ files.

  Dataset EGAD50000001406

• prostate cancer plasma cfRNA

  Dataset contains mRNA capture sequencing data from plasma of 180 different human donors: 132 prostate cancer patients (PRAD) and 48 cancer-free controls. Samples were sequenced on a NovaSeq X and sequencing data is provided in FASTQ format.

  Dataset EGAD50000001805

• Exome Sequencing data from infertility cases.

  This dataset includes exome sequencing (ES) from a cohort of patients with infertility. Sequencing was performed on genomic DNA extracted from blood, using Agilent SureSelect XT Low Input exome capture and Illumina NovaSeq 6000 paired-end sequencing and is intended to facilitate research into novel genetic causes of infertility.

  Dataset EGAD50000001881

• UK_exomechip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC exomechip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper

  Dataset EGAD00010002019

• UK_immunochip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC immunochip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper.

  Dataset EGAD00010002049

• Dataset of Recurrent resistance mutations to lirafugratinib delineate treatment sequences for FGFR2-driven tumors

  This dataset is made of 23 pairs of RNAseq and 36 pairs of Exome-seq, both sequenced from Illumina Novaseq. This includes 47 samples, composed of 25 tumors, 13 healthy and 9 xenograft

  Dataset EGAD50000001981

• Flexible and rapid validation of structural variants using adaptive sampling

  This is the DAC that oversees the application and approval process for access to the Oxford Nanopore fastq files associated with the study, "Flexible and rapid validation of structural variants using adaptive sampling". The DAC members include Dr. Stephen W. Scherer (swscherer@sickkids.ca) and Dr. Lars Feuk (lars.feuk@igp.uu.se).

  Dac EGAC50000000748

• CD8+ Tumor-Infiltrating Lymphocyte Abundance is a Positive Prognostic Indicator in Nasopharyngeal Cancer

  This retrospective tissue study explores the prognostic significance of tumour-infiltrating lymphocyte (TIL) populations in NPC, using a combination of RNA sequencing and immunohistochemistry.

  Study EGAS00001006396

• Untargeted serum metabolomics profiled by Metabolon Inc.

  Raw untargeted metabolomics profiled by Metabolon Inc. for 540 samples from healthy individuals. Files include sample names and run details which can be matched to their metagenomic sequencing samples from PRJEB11532 and PRJEB17643. Information regarding metabolite metadata is also available, including

  Dataset EGAD00001006247

• Oncoprint GSCCs

  This dataset contains DNA sequencing data from 7 GSCCs (data for BT569 is not available). We performed focused exome sequencing (43 most mutated genes in GBM), combined with OneSeq analysis (Agilent) on the GSCCs and identified both shared and GSCC-specific mutations. For CME038, whole genome sequencing was performed.

  Dataset EGAD00001011276

• CYPTAM - PacBio SMRT sequencing

  Dataset contains CYP2D6 sequencing data of 566 individuals who used tamoxifen as adjuvant breast cancer therapy. Phenotype data consists of the ratio between the metabolites endoxifen and desmethyltamoxifen (Metabolic ratio (MR)) as a proxy for CYP2D6 enzyme activity. Each sample is linked to one bam-file containing the CYP2D6 sequence.

  Dataset EGAD00001005972

• WGS of off-target analysis of prime editing in organoids

  Five edited and two unedited organoid clones with one clone prior to editing were paired-end whole genome sequenced using Illumina Novaseq 6000 system. The reads were mapped to hg38 genome assembly and data is provided as BAM files.

  Dataset EGAD00001007744

• Whole-genome sequencing of BCR-ABL1 lymphoblastic leukemia

  This dataset is derived from whole-genome sequencing (WGS) of DNA from 57 BCR-ABL1 lymphoblastic leukemias (53 diagnostic, 4 relapse) and 53 germline samples.

  Dataset EGAD00001010323

• Sporadic Parathyroid Carcinoma

  This dataset is compromised of 5 sequencing experiments from a single patient with sporadic and recurring parathyroid carcinoma. The samples include whole genome sequence of the primary tumor, the first recurrent tumor and peripheral blood. Whole transcriptome sequence of the first and second recurrent tumors are also included.

  Dataset EGAD00001000370

• Somatic pseudogenes acquired during cancer development – RNAseq

  Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.

  Dataset EGAD00001000639

• ICR_RNASeq_pHGG

  RNA sequencing of paediatric high grade gliomas and diffuse intrinsic pontine gliomas. RNA was sequenced from fresh frozen surgical material or from primary cells cultured under stem cell conditions. RNA was subjected to Illumina whole transcriptome paired end sequencing. Data is provided as paired-end FASTQ files

  Dataset EGAD00001004116

• Genetic and epigenetic characterization of adenoid cystic carcinoma

  Whole genome sequences of ACC primagrafts, Histone modification maps and transcription factor binding maps for ACC primagrafts and primary tumors. Processed ChIP-seq data is available on GEO under accession number GSE76465.

  Dataset EGAD00001001662

• Illumina sequencing of V4 variable region of the 16S rRNA from human feces samples

  The dataset is composed of 62 samples (31 subjects before and after probiotic-like bacteria treatment). Sequencing was performed using Illumina HiSeq 2500. Fastq files are provided.

  Dataset EGAD00001004944

• Role of HPV and Interferon in APOBEC mutational signature (2019-04-11)

  The aim of this project is to test whether HPV oncogenes and /or interferon induce the APOBEC mutational signature in vitro, and to test the role of APOBEC3A in this process. . This dataset contains all the data available for this study on 2019-04-11.

  Dataset EGAD00001004955

• Immunoglobulin sequences of self-reactive plasma cells in celiac disease

  Paired immunoglobulin heavy and light chain sequences were obtained from 803 single IgA plasma cells isolated from duodenal biopsies of five celiac disease patients. The cells were specific to discrete antigenic regions of the enzyme TG2, which is the main autoantigen in celiac disease.

  Dataset EGAD00001005029

• Comparison of 133/144bp dominant phenotype vs 166bp dominant phenotype.

  The sequencing results provided in this study is enriched through liquid phase hybridization capture. The data set shows 35 clinical cfDNA samples showing a dominant peak at 166bp and 35 clinical cfDNA samples showing a dominant peak at 134/144bp.

  Dataset EGAD00001005798

• EGAD00010000628

  The TEENAGE study target population comprised adolescent students aged 13 to 15 years attending the first three classes of public secondary schools located in the wider Athens area of Attica.

  Dataset EGAD00010000628

• Average_hypermethylation_TF_sites

  Average hypermethylation on transcription factor binding sites based on nanopolish calls; only positions showing higher methylation than sample’s average methylation at enhancers were included when defining the average methylation level. Data from 6 individuals at different time points.

  Dataset EGAD00010002411

• Whole Genome - Uveal Melanoma

  Whole genome sequencing on 1 uveal melanoma and corresponding germline sample. Libraries were prepared using the Kapa HyperPrep kit (Roche, 07962363001). Paired-end libraries (2 x 150 bp) were sequenced on a NovaSeq 6000 instrument (Illumina).

  Dataset EGAD50000000764

• Massive genomic rearrangement acquired in a single catastrophic event during cancer development

  Massive genomic rearrangement acquired in a single catastrophic event during cancer development

  Dataset EGAD00001000002

• DAC-2023-07-05-Ritz (DAC-007)

  Full description of the dataset and all necessary information on metadata may be found under (https://zenodo.org/records/11237107): DAC-2023-07-05-Ritz (DAC-007), raw data in EGA, metadata in Zenodo (https://zenodo.org/records/11237107)

  Dataset EGAD50000001147

• Analysis of Multiparametric MR imaging and tumor tissue sampling to identify response and acquired resistance to HIF-2 inhibition in patients with advanced clear cell renal cell carcinoma enrolled in a phase 1, multiple-dose, dose-escalation trial of PT2385, a HIF-2alpha inhibitor

  Study EGAS00001003506

• RNA-Seq soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001008467

• Triple-negative breast cancer sequencing data

  Single-cell RNA sequencing and spatial transcriptomic sequencing data associated with manuscript 'Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity'

  Dataset EGAD50000002266

• HV31 - 10x linked-read sequencing

  10x linked-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~40×. Sequencing was performed at Bart’s and the London Genome Centre on the Illumina HiSeq platform.

  Dataset EGAD00001007046

• 10x Genomics Single Cell Gene Expression for SA1035X8XB03425

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 8

  Dataset EGAD00001009148

• 10x Genomics Single Cell Gene Expression for SA1184SA

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient SA1184

  Dataset EGAD00001009145

• 10x Genomics Single Cell Gene Expression for OV2295

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma cell line OV2295

  Dataset EGAD00001009143

• Single Cell Genome Sequence for DLP+ library A96141A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 8 on DLP+ library A96141A

  Dataset EGAD00001009777

• Genome-wide array data Tunisia and Morocco

  This dataset contains genome-wide array data from Tunisian and Moroccan individuals. Tunisian individuals were sampled in the city of Tunis (n = 64), and Moroccan individuals in different urban areas in the country (n = 45).

  Dataset EGAD00001009071

• 10x Genomics Single Cell Gene Expression for SA604X8XB02164

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA604 passage 8

  Dataset EGAD00001009118

• The University of Hong Kong Gastric Cancer XClone Study Single Cell CNV Data

  Single cell encapsulation and DNA libraries were prepared by Chromium™ Single Cell DNA Reagent Kits and Chromium™ Single Cell C and D Chip Kits.

  Dataset EGAD00001015383

• 10x Genomics Single Cell Gene Expression for SA1035X4XB02879

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 4

  Dataset EGAD00001009147

• Multiome

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Multiome Experiments

  Dataset EGAD00001009824

• 200PT : SNV vcf files

  200PT : SNV vcf files. SNV calls generated using SomaticSniper and PhyloWGS, from the CPCGene 200PT Subclonality study

  Dataset EGAD00001004072

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - TLR_pathway_study

  upcoming publication

  Dataset EGAD00001001960

• CNA vcf files for CPCG Subclonal Heterogeneity

  CNA calls generated using the SomaticSniper-Battenberg-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study

  Dataset EGAD00001004405