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• EGAD00000000057

  WTCCC project samples from the Parkinson's disase cohort

  Dataset EGAD00000000057

• Anaplastic Thyroid Cancer somatic variants (SomaticSniper)

  Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with SomaticSniper. Somatic variant calls are in VCF format. In total there are 94 tumour samples, each with a matched normal.

  Dataset EGAD00001004128

• HIPO blastemal Wilms (nephroblastoma) CHIP sequencing samples

  HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving events caused by differential SIX1 binding of the SIX1 Q177R mutatns

  Dataset EGAD00001000992

• Whole exome sequencing of Finnish hereditary breast cancer families

  Dataset contains Whole Exome Sequencing(WES) data from 37 individuals as aligned bam-files. The reads have been aligned using bowtie2 to human genome hg19 build.

  Dataset EGAD00001002133

• cHCC-ICC WES

  The whole exome sequencing data of 291 tumor/normal samples from 121 cHCC-ICC cases.

  Dataset EGAD00001005183

• postcovid19

  contain the raw data from scRNA, scATAC, genotyping.

  Dataset EGAD00001008122

• Germline WES data of parents whose children have germline CHEK2 mutations

  This data set includes bam files (aligned to hg38) from the germline of parents whose children have CHEK2 germline mutations.

  Dataset EGAD00001009516

• Germline WES data of children with pathogenic mutations in cancer predisposing genes

  This data set includes bam files (aligned to hg38) from the germline of children who have pathogenic mutations in cancer predisposing genes

  Dataset EGAD00001009854

• Pathology and tumor biology DAC

  Dac EGAC00001003221

• CDH Asian Head and Neck Angiosarcoma

  Dac EGAC00001003145

• Relapsed and Primary Neuroblastoma DAC

  Dac EGAC00001000373

• Illumina - Population and Medical Genomics Group

  Dac EGAC00001000686

• ICR_Evolutionary Genomics and Modelling

  Dac EGAC00001001050

• RNAseq intra- and extracranial ECs DAC

  Dac EGAC00001001622

• Gene expression and Cancer

  Dac EGAC00001001772

• Neuroblastoma and cell migration DAC

  Dac EGAC00001001965

• Genome-wide data Resande and Swedes

  Dac EGAC00001002627

• INSERM U944 Team Genome and Cancer

  Dac EGAC00001002976

• Cell-free DNA sequencing using newly developed single-strand DNA library preparation

  We performed whole genome sequencing of cell-free DNA that was collected from human plasma using an improved cfDNA purification protocol and DNA library prepared with newly developped protocol of our own.

  Study JGAS000257

• Whole genome sequencing data of relapsed paediatric KMT2A-rearranged acute lymphoblastic leukemia

  Whole genome sequencing data of relapsed KMT2A-rearranged leukemia. Dataset includes bam-file of released case. Diagnostic (ALLT-375D) and remission (ALLT-375R) samples can be found with EGA ID: EGAD50000001568.

  Study EGAS50000001100

• 10X Genomics single-nuclei RNA-sequencing of endometrium from women with and without PCOS

  Chromium Next GEM Single Cell 3’ Gel Bead Kit (Dual Index) v3.1 (10X Genomics) of endometrium from 27 women including 5 without PCOS and 12 with PCOS. Following baseline biopsies, PCOS participants underwent a 16-week randomized controlled trial with metformin (n=7) or lifestyle intervention (n=3). 25,000 raw reads per nucleus

  Dataset EGAD50000001017

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are WGS data generated from differentiated neural stem cells (NSCs) of NXPG-32 patient (XPG patient with neurodegeneration) and a matched healthy control CTRL-33.

  Dataset EGAD50000000232

• mCEL-Seq2 analysis of human brain tissues and border regions

  mCEL-Seq2 analysis with reference mapping of human brain tissues and border regions

  Dataset EGAD50000000046

• Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

  Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Here we report analysis of gene mutation, copy number and RNA expression of 57 sporadic well-differentiated pNETs.

  Study EGAS00001003038

• RNA seq of MPNST tumour samples

  RNA sequencing of 10 MPNST tumour samples as part of a larger study of MPNST. Article: Lyskjær et al, 2020, J Pathol, "H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours".

  Study EGAS00001004528

• Genetic Basis of Hepatosplenic T Cell Lymphoma (HSTL)

  Whole exome sequencing of hepatosplenic T cell lymphoma (HSTL) tumors, paired normals, and cell lines, including (1) 68 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL tumor samples, (2) 20 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL paired normal samples, and (3) 2 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL cell lines.

  Dataset EGAD00001003246

• Exome sequencing and RNAseq data

  Whole Exome Sequencing of 9 Colorectal Cancer (CRC) samples performed on Illumina HiSeq4000 consisting of aligned paired reads. RNAseq data sequenced on Illumina NextSeq500 consisting of FASTQ single reads from 3 CRC colon samples. A total of 12 samples from five patients (we matched normal tissue or pbmc and tumors) were sequenced on Illumina NextSeq500.

  Dataset EGAD00001003788

• RNA-seq data: Histone mutations in human Pre-Leukemic HSC and AML

  RNA-seq data from TEX cells transduced with HIST1H3H WT, HIST1H3H K27M, HIST1H3F WT, HIST1H3F K27I and Luc2 control in triplicate. In addition, RNA-Seq was performed on untransduced TEX cells. Libraries [rRNA-depleted stranded (HMR)] were sequenced on an Illumina Hiseq 4000 platform to generate 100 bp paired-end reads.

  Dataset EGAD00001004437

• Human lymphoma plasma cfRNA - raw data

  This study contains total RNA sequencing data from plasma of 65 different human donors: 30 diffuse large B-cell lymphoma patients, 13 primary mediastinal large B-cell lymphoma patients and 22 cancer-free controls.

  Study EGAS00001007127

• Whole genome sequencing on HiSeq platform of melanocytic nevi and normal sample pairs from 14 cases

  Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 28 samples: matched tumour-normal pairs from 14 melanocytic nevi cases

  Dataset EGAD00001004474

• H3K27me3 ChIP-Seq of 6 samples and H3K27ac ChIP-Seq of 4 samples with respective input controls

  H3K27me3 ChIP-Seq of 6 samples and H3K27ac ChIP-Seq of 4 samples with respective input controls

  Dataset EGAD00001004992

• Myeloid gene panel or whole exome sequencing data on blood and bone marrow of 15 individuals with germline RUNX1 mutations to characterize additional somatic mutations.

  This dataset consists of 20 fastq files in total from exome and myeloid gene panel sequencing of 15 carriers of germline RUNX1 mutations from 10 different families.

  Dataset EGAD00001006010

• Targeted sequencing data of peripheral blood mononuclear cells obtained from 4 ATL patients and 10 HTLV-1-infected asymptomatic carriers.

  Targeted capture sequencing data of peripheral blood mononuclear cells (PBMCs) obtained from 4 ATL patients (6 samples) and 10 HTLV-1-infected asymptomatic carriers.

  Dataset EGAD00001007031

• Whole Exome Sequencing of Mixed Histology Lung Cancer

  We conducted whole-exome sequencing (WES) and microarray profiling on 19 micro-dissected tumor regions of different histologic subtypes from 9 patients with lung cancers of mixed histologic patterns including 6 LUAD, 6 LCNEC, 3 SCLC, 3 LUSC, and one poorly differentiated NSCLC-NOS.

  Dataset EGAD00001007076

• Baseline and progression dataset

  RNAseq FASTq files from 44 pre-treatment (Ven-Obi or Clb-Obi) and 44 paired, post-treatment relapsed CD19+ B cells.

  Dataset EGAD00001009419

• Single-cell RNA-seq of cervical smears and early placental material

  Fastq files of single-cell RNA-sequencing data generated with 10X Genomics of twelve non-invasive cervical samples from pregnant women (7-12 weeks gestational age) and six placental biopsies from patients who had a recurrent miscarriage early during gestation (<12 weeks gestational age).

  Dataset EGAD00001010094

• Long read mRNA sequencing of blood cells exposed to different immune stimuli

  Long-read (PacBio) RNA sequencing dataset of in vitro stimulated PBMC cells. 5 samples consisting of 1 RPMI control and 4 stimulus conditions (lipopolysaccharide (LPS), polyI-polyC, S. aureus and C. albicans) all originating from one donor. Files are raw BAM format files generated by Sequel 2 machine.

  Dataset EGAD00001009998

• TGL49 LFS CHARM panel

  Targeted panel sequencing of hereditary cancer syndrome-associated genes (TP53, BRCA1, BRCA2, PALB2, MLH1, MSH2, MSH6, PMS2, EPCAM, and APC) in plasma and buffy coat samples from patients with Li-Fraumeni syndrome.

  Dataset EGAD00001010011

• Single-cell long-read transcriptomes from CH, MDS and AML patients with CH mutations

  Single-cell long-read (ONT) transcriptome sequencing from CH (n = 3), MDS (n = 5, MDS02 in 2 replicates) and AML (n =1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8, U2AF1 n = 1) or transcription regulators (DNMT3A - CH04). Full length cDNA from 10x Genomics 3' V3.

  Dataset EGAD00001011282

• Paired ONT and downsampled Illumina cfDNA dataset

  Dac EGAC00001002860

• Tumor-Normal matched colon adenomas and carcinomas

  Dac EGAC00001003248

• Microenvironment in lymphoma pathogenesis and therapy - DAC

  Dac EGAC00001003228

• Leucocyte eQTLs in autoimmune disease and health

  Dac EGAC00001000338

• Multiple esclerosis and mixed microbial infections DAC

  Dac EGAC00001000892

• 16S rRNA gene amplification and maternal factors DAC

  Dac EGAC00001000931

• Pathology and tumor biology

  Dac EGAC00001001923

• Sarcoma biology and genomics data access commitee

  Dac EGAC00001002609

• Sarcoma biology and genomics data access committee

  Dac EGAC00001002610

• Pheochromocytoma and paraganglioma single nuclei RNA-seq

  Dac EGAC00001002657

• Computational Cancer Genomics and Tumor Evolution Group

  Dac EGAC00001002722

• MSAT and JMS Data Access Committee

  Dac EGAC00001002734

• Human islet sQTL and eQTL DAC

  Dac EGAC00001002796

• Genomics and Oncogenesis of Pediatric Brain Tumors

  Dac EGAC00001003123

• DAC Bone and soft tissue tumor pathology

  Dac EGAC50000000228

• RNASeq Javelin head and neck 100

  Study EGAS00001007497

• PacBio HiFi whole-genome sequencing of two microsatellite instability (MSI) gastric cancer

  We generated long-read whole-genome sequencing (WGS) data using PacBio HiFi from two human gastric cancer cell lines exhibiting microsatellite instability (MSI). The dataset contains aligned bam (hg38) files.

  Dataset EGAD50000002300

• Spatially resolved targetted sequencing of colorectal cancers

  Sequencing of laser-capture micro dissected colorectal tumour glands using a targeted capture panel. Tumours were previously subjected to WGS in the parent EPICC study. UMI-resolved aligned bam files, aligned to hg38.

  Dataset EGAD50000001650

• Long-read RNA-seq from 5 patients with stereotyped subset CLL

  Oxford Nanopore Technologies based long-read RNA sequencing data from 5 patients with stereotyped subset CLL. The BAM files were aligned against hg19 reference genome.

  Dataset EGAD50000000755

• Deep Sequencing of somatic cancer mutations

  We enriched a panel of cancer associated genes using the Custom Sure Select Target Enrichment Kit. Identified mutations were validated with deep sequencing in order to assess mutated allele frequencies more accurately.

  Dataset EGAD00001001313

• RNA-Seq of human CD4 Treg cells

  This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole transcriptome data for141 samples. The final quality filtered set included 123 individuals with RNA-seq data.

  Dataset EGAD00001004830

• HSP90 inhibitor resistant K562 cells

  K562 cell line has been treated with two different HSP90 inhibtors. After resistance clones emerged, they have been genetically characterized using WES in comparison to the parental K562 cell line.

  Dataset EGAD00001009051

• Human primary and metastatic colorectal cancer (CRC) samples

  Dac EGAC00001002954

• NCCS-NSCLC-ITH2 project leader and principal investigator

  Dac EGAC00001003152

• Department of Gastroenterology and Hepatology Data Access Committee

  Dac EGAC00001003361

• Shanghai Institute of Endocrine and Metabolic Diseases

  Dac EGAC00001000677

• KUL Research group Molecular Bacteriology and Beneo Orafti.

  Dac EGAC00001000706

• Primary tumor and metastatic breast cancer data access

  Dac EGAC00001001687

• DKFZ OE0436 and UNI-Klinikum Heidelberg DAC

  Dac EGAC00001001904

• Haematopoietic stem cells and malignancies Data Access Comittee

  Dac EGAC00001002410

• DAC Genome-wide array data Tunisia and Morocco

  Dac EGAC00001002770

• France

  French cases and controls

  Dataset EGAD00010002023

• Belgium

  Belgian cases and controls

  Dataset EGAD00010002022

• Finland

  Finnish cases and controls

  Dataset EGAD00010002020

• Genomics and Oncogenesis of Pediatric Brain Tumors

  Dac EGAC00001003200

• Department of Gastroenterology and Hepatology Data Access Committee

  Dac EGAC00001003021

• Single-Cell NSC DAC – ADHD and Control iPSC Study

  Dac EGAC00001003572

• Walter and Eliza Hall Institute Research Data Access Committee

  Dac EGAC00001003583

• LUMC Department Cell and Chemistry Biology, Diabetes Group

  Dac EGAC50000000905

• A Pilot Study of NKTR-214 and Nivolumab in Selected Patients with Locally Advanced/Metastatic Sarcoma

  Study cohort comprises samples derived from patients that received treatment on an open-label, non-randomized, non-comparative pilot study of bempegaldesleukin, a CD122-preferential interleukin-2 pathway agonist, with nivolumab in refractory sarcoma at Memorial Sloan Kettering/MD Anderson Cancer Centers (NCT03282344). Patient tumors include a variety of sarcoma subtypes. Samples include whole exome sequencing of tumor/normal pairs, poly-A RNA and TCR sequencing of tumors.

  Study phs002852

• Whole genome sequencing data of paediatric ETV6-RUNX1 acute lymphoblastic leukemia

  Whole genome sequencing data from paediatric (<18-y) ETV6-RUNX1 fusion positive acute lymphoblastic leukemias. Dataset includes fastq and BAM files from diagnostic and remission (control) samples of 33 patients. Dataset consists of two experiments depending on sequencing instrument; "Experiment 1" sequenced by using Illumina Hiseq X Ten instrument, and "Experiment 2" Illumina Novaseq 6000, respectively.

  Dataset EGAD00001010128

• Investigation of Human DNA Replication Timing Variation by Whole Genome Sequencing

  To study inter-individual variation in human DNA replication timing, we performed whole-genome sequencing of human pluripotent stem cell lines. This data was used to infer replication timing and link them to genetic polymorphisms.

  Study phs001957

• Genomic Profiling Reveals Heterogeneous Populations of Ductal Carcinoma In Situ

  Whole Exome Sequencing(WES) and copy number variation(CNV) analysis were performed using breast samples collected from non-invasive breast cancer patients in order to analysis of somatic mutations related to breast tumor phenotypes.

  Study JGAS000202

• WGS of IPMN-PDAC Data

  This study investigates IPMN-PDAC development using whole-genome sequencing (WGS) data from 42 tumours collected from multiple regions and 12 matched normal samples. Sequencing was performed on Illumina platforms with 150 bp paired-end reads.

  Study EGAS50000001182

• MEMORI WES bams

  This project stores bam files from deep whole exome sequencing from oesophageal adenocarcinoma at different timepoints during neoadjuvant treatment (prior, during, post treatment), which were used to analyse evolutionary and phenotype dynamics in oesophageal adenocarcinoma during neoadjuvant treatment.

  Study EGAS50000000240

• Longitudinal evaluation of circulating tumor DNA in early breast cancer receiving neoadjuvant systemic therapy using a tumor-informed assay

  This study evaluates a highly sensitive tumor-informed ctDNA assay in a real-world cohort of patients receiving neoadjuvant therapy (NAT) to assess clinical validity and explores prognostic outcomes

  Study EGAS50000000771

• Predictors of Immune Checkpoint Blockade Response in dMMR Colorectal Cancer Using an Integrated Immune-Enhanced Multi-Omics Platform

  To identify candidate tumor- and immune-related biomarkers associated with clinical outcomes following anti–PD-1 therapy in dMMR colorectal cancer, we conducted a comprehensive genomic profiling using ImmunoID NeXT platform, including whole exome, whole transcriptome and TCR/BCR sequencing.

  Dataset EGAD50000002504

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are time series bulk RNA-seq data generated from isogenic wild-type (WT), XPA and XPG gene knockouts hiPSC cells during cortical neuronal differentiation.

  Dataset EGAD50000000228

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are time series bulk RNA-seq data generated from XP patients and controls as well as rescued patient hiPSC cells during cortical neuronal differentiation.

  Dataset EGAD50000000230

• Lung_Multi_site_Targeted_Sequence_Capture

  DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Study EGAS00001000436

• Multisite_Primary_Breast_Cancer

  DNA extracted from multiple biopsies taken from different areas of primary breast tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Study EGAS00001000891

• Whole genome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

  Whole genome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

  Dataset EGAD00001003115

• DDD DATAFREEZE 2016-10-03: 7832 trios - phenotypic and family descriptions

  DDD DATAFREEZE 2016-10-03: 7831 trios - phenotypic and family descriptions

  Dataset EGAD00001003350

• DDD DATAFREEZE 2014-11-04: 4293 trios - phenotypic and family descriptions

  DDD DATAFREEZE 2014-11-04: 4293 trios - phenotypic and family descriptions

  Dataset EGAD00001001977

• Whole-Exome Sequences Tunisian Imazighen and non-Imazighen

  Dataset with 55 whole-exome sequences from Tunisian non-Imazighen samples and 20 whole-exome sequences from Tunisian Imazighen samples.

  Dataset EGAD00001007511

• Newcastle COVID-19 Single-cell PBMC

  Single-cell multi-omic profiling of healthy controls, asymptomatic and hosptial-admitted COVID19 patients recruited from Newcastle University hospitals. These data also include healthy control volunteers treated with IV-LPS as inflammatory controls. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors.

  Dataset EGAD00001007866

• Whole genome sequencing of brain AVM endothelial and non-endothelial cell fractions

  Whole genome sequencing data of brain AVM endothelial and non-endothelial cell fractions, as well as paired blood samples

  Dataset EGAD00001009696

• Transcriptome profiling of human lung fibroblasts in COPD

  Primary lung fibroblast were isolated from well-matched control donors (no COPD, n=3) and patients with COPD (GOLD stage I-IV, n=8). Total RNA of cultured human lung fibroblast were isolated at passage 3 and rRNA was depleted. 75 bp single-end reads were generated from RNA libraries on Illumina NextSeq 500.

  Dataset EGAD00001009405

• H3K27ac ChIP-seq of human acute leukemias and healthy donors

  H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included.

  Dataset EGAD00001011060

• CML-SC and HSC study data access committee

  Dac EGAC00001003028

• European Network of Genomic and Genetic Epidemiology Data Access Committee

  Dac EGAC00000000008