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• DAC Molecular heterogeneity and commonalities in pancreatic cancer precursors with gastric and intestinal phenotype

  Dac EGAC00001002978

• RNA sequencing of CD8 T cells from melanoma patients prior to and during checkpoint immunotherapy and untreated healthy controls

  We are interested in inter-individual variation in transcriptional response to immune checkpoint blockade. We have analysed poly A purified RNA expression from CD8 T cells (297 transcriptomes in total) isolated from metastatic melanoma patients (n=106) prior to and during treatment with either single agent (Pembrolizumab) or combination (Ipilimumab/ Nivolumab) immune checkpoint blockade. We compare expression at different stages of treatment and additionally contrast this with that from healthy controls (n=68).

  Study EGAS00001004081

• Transcriptomic analysis of human hematopoietic populations sorted from umbilical cord blood.

  We isolated by fluorescence-activated cell sorting highly purified populations (long term hematopoietic stem cells (LT-HSCs), short term hematopoietic stem cells (ST-HSCs), multipotent progenitors (MPPs), common myeloid progenitor (CMPs), granulocyte and monocyte progenitors (GMPs), multilymphoid progenitors (MLPs), Myeloid-erythorid Progenitor (MEP), Granulocytes, Monocytes, B cells, T cells, Dendritic cells, Natural Killer cells and Erythrocyte Progenitors from 3 to 4 cord blood pools. We extracted RNA from 5K cells of each population and performed RNA-sequencing.

  Study EGAS00001004968

• Data Access Committee - cfDNA fragmentation and personalized sequencing reveal ctDNA in urine and plasma of glioma patients

  Dac EGAC00001001593

• BRCA2, ATM, and CDK12 defects differentially shape prostate tumor driver genomics and clinical aggression

  Study EGAS00001004800

• The Institute of Cancer Research - Endocrinology Team

  Dac EGAC00001000532

• The Ashkenazi Genome Consortium Data Access Committee

  Dac EGAC00001000151

• The EMC-ILC3 consortium Data Access Committee

  Dac EGAC00001000729

• The Xiaoping Miao's lab of HUST.

  Dac EGAC00001000897

• Lead investigator of the TONIC study

  Dac EGAC00001001150

• The Jerusalem Perinatal Study (JPS) data access committee

  Dac EGAC00001001421

• Head of the circulating cells platform

  Dac EGAC00001001508

• Cancer Genomics of the Kidney - Targeted Sequencing

  Dac EGAC00001003091

• Spatial Dynamics of the Developing Human Heart

  Dac EGAC50000000616

• Genomic Analysis of Metastatic Brain Cancer

  This study contains targeted exome and transcriptome sequencing of metastatic brain tumors from 68 patients. Sequencing data includes i) targeted Tempus xT exome sequencing from matched tumor/normal from 68 patients, and ii) whole-transcriptome RNA sequencing from a subset of 65 patients.

  Study phs002639

• Whole genome sequencing of preneoplasia lung adenocarcinoma

  Whole genome sequencing of 42 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=5), adenocarcinoma in situ (AIS, N=7), minimally invasive adenocarcinoma (MIA, N=6) and invasive lung adenocarcinoma (ADC, N=8) and adjacent lung tissues (Normal, N=16).

  Study EGAS50000000272

• Nasal Polyp RNAsequencing, Skaraborg Sweden

  Whole-transcriptome sequencing (RNAseq) in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and controls. Differential expression patterns in genes involved in cilia, viral defense and NKT-cell specific pathways, suggesting a role of viral immunity in combination with cilia functionality in CRSwNP.

  Study EGAS00001007088

• ATAC-seq dataset of patient and healthy donors

  ATAC-seq dataset on a patient (P) presenting with defects of immunity and two (C5, C6) healthy donors. This dataset contains raw and processed files from ATAC-seq chromatin accessibility analysis. There are 3 single-read (50 bp) fastq files (1 per patient/ donor). Processed files consist of narrowPeak files (1 per patient/ donor) and one file that contains read counts in consensus peaks.

  Dataset EGAD00001008370

• ChIP-Seq on multiple myeloma and plasma cell leukaemia cell lines

  ChIP-seq data (H3K4Me1, H3K4Me3, H3K27Ac histone modifications) in experimental triplicates on multiple myeloma cell line KMS11 and plasma cell leukaemia cell lines L363 and JJN3. ChIP reactions were performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal Kit. ChIP libraries were generated using HTP Illumina library preparation kit, and sequenced using Illumina HiSeq 2000 with 100 bp single-ended reads. ChIP-seq files are in BED format.

  Dataset EGAD00001003349

• Co-infection of fungi and bacteria in brain tissue from elderly persons and patients with Alzheimer's disease.

  Dac EGAC00001000797

• PBAT sequencing of cytotrophoblast and mural trophectoderm

  PBAT sequencing of primary first trimester cytotrophoblast and mural trophectoderm

  Dac EGAC50000000424

• Evolutionary trajectories and clonal migration underlying tumor progression and lymph node metastasis in resectable lung cancer

  Study EGAS00001005242

• iOmics_genomic_data

  iOmics genomic data using 2.5M and Exome array

  Dataset EGAD00010001309

• Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants

  We discover numerous associations between human leukocyte antigen (HLA) variation and a comprehensive set of phenotypes derived from electronic health records.

  Study phs001949

• MicroC in KMS11 and TKO cells

  MicroC to show high resolution chromatin interactions in t(4;14) Myeloma cell line KMS11 and KMS11 cells with knock-out of translocated NSD2 allele (KMS11 TKO).

  Study EGAS50000000078

• Genetic analysis of non-small cell lung cancer patients and PDX tumor harboring driver gene alteration

  Genetic analysis of non-small cell lung cancer patients and PDX tumors with EGFR mutation, ALK fusion, ROS1 fusion, etc.

  Study JGAS000413

• Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends

  Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends

  Study EGAS00001001882

• Single cell RNA-sequencing of GSCs and GBM tumours

  Characterization of glioblastoma tumors and glioblastoma stem cell (GSCs) lines with single cell or single nuclei RNA-sequencing.

  Study EGAS00001004656

• RNA sequencing of AD, MCI and control OM cells

  Total RNA sequencing of cultured OM cells derived from patients with Alzheimer's disease (AD), individuals with mild cognitive impairment (MCI) and cognitively healthy controls.

  Study EGAS00001006195

• Nanopore whole-genome sequencing of human bone and soft-tissue sarcomas

  We performed single and multi-region nanopore whole-genome sequencing on human bone and soft-tissue sarcoma samples. We also performed nanopore whole-genome sequencing on matched whole blood samples.

  Dataset EGAD50000001392

• Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols

  This dataset contains single-cell RNA sequencing and time-course bulk RNA sequencing data of brain organoids grown from multiple cell lines using four different protocols recapitulating dorsal and ventral forebrain, midbrain, and striatum.

  Dataset EGAD50000000938

• 3_eCLIP_TDP-43

  eCLIP of TDP-43 from iPSC-derived motor neurons in 2 control lines. Per line input and IP samples and analysis including bigWig files and peak files.

  Dataset EGAD00001008426

• Clinical data

  Clinical data from GO30140 group A and group F and IMBrave150 biomarker populations including gender, confirmed RECIST response by independent review forum (IRF), overall survival (OS), progression survival by IRF, treatment group and treatment

  Dataset EGAD00001008130

• Single-cell paired sequences from intraepithalial CD8+ αβ T-cells from celiac disease patients and controls

  Paired T-cell receptor sequences sequenced from single cells, from intraepithalial CD8+ αβ T-cells. Sequences are from from untreated and treated (on a gluten-free diet) celiac disease patients and controls.

  Dataset EGAD00001006900

• Familial adult myoclonic epilepsy type 1 in Sri Lankan and Indian families

  Whole genome sequencing data from four affected and one unaffected individuals from two families with familial adult myoclonic epilepsy, one of Sri Lankan origin and one of Indian origin. BAM files aligned to hg19 reference genome.

  Dataset EGAD00001005777

• WES of mCRC xenografts under cetuximab treatment.

  WES on cetuximab treated, untreated and release samples of two metastatic colorectal xenografts. First case: 3 cetuximab treated samples, 3 placebo and 3 release. Second case: 2 cetuximab treated samples, 2 placebo and 3 release. Paired fastq.

  Dataset EGAD00001005186

• Transcriptomic and epigentic analysis of human peripheral blood NK cell subsets revealing role of Bcl11b in differentiation

  Transcriptomic analysis of seven human peripheral blood NK cell subsets and three T cell subsets purified from healthy cytomeglovirus seropositive donors. Epigenetic analysis including identification of open chromatin and active enhancer elements confirms key regulatory factors defining an NK cell differentiation axis. Chromatin-immunoprecipitation sequencing reveals contribution of key transcription factors associated with NK cell differentiation including Bcl11b.

  Study EGAS00001005025

• THE SAHEL 2.5 MILLION SNP ARRAY

  Dac EGAC00001000427

• The NOWAC study Data Access Committee

  Dac EGAC00001000521

• The Ovarian Cancer Association Consortium Data Access Committee

  Dac EGAC00001000616

• The Kibbutzim Family study (KFS) data access committee

  Dac EGAC00001000805

• Present-day genomics from the Eurasian steppe

  Dac EGAC00001000878

• Genome Dynamics in the Immune system lab-imagine

  Dac EGAC00001001254

• DAC the Tel-Aviv Medical Center Neurosurgery dept

  Dac EGAC00001002176

• DAC Genetic variability in the glucocorticoid receptor NR3C1

  Dac EGAC00001002382

• The Solomon Islands: Human Origins array genotype data

  Dac EGAC00001002588

• The Swedish Childhood Tumor Biobank DAC

  Dac EGAC50000000095

• Hi-C on the OCIAML-2 Cell Line

  Study EGAS00001004743

• Age_Validation

  Rounded chronological age of the participants

  Dataset EGAD00010002753

• Age_TrainTest

  Rounded chronological age of the participants

  Dataset EGAD00010002755

• Establishment and characterization of a new Pseudomonas aeruginosa infection model using 2D airway organoids and dual RNA sequencing

  Study EGAS00001007463

• Novel genome editing strategies to uncover genotype-phenotype correlations in Polycystic Kidney Disease: a proof-of-concept

  Bulk RNA-seq of genome-edited HEK293T cell lines engineered to model specific PKD1 variants. This dataset enables the exploration of genotype-phenotype correlations in Polycystic Kidney Disease (PKD)

  Study EGAS50000001188

• RNA Sequencing of Colorectal Liver Metastases

  A subset of patients with metastatic colorectal cancer achieves prolonged survival after hepatic resection of limited liver metastases. Here, we examined the molecular features of colorectal liver metastases as they relate to clinical outcomes.

  Study EGAS00001002945

• ATAC-seq/ChIP part

  Epigenetics: ATAC-seq and ChIP-seq data

  Study EGAS00001006520

• Deep MRD profiling defines outcome and unveils different modes of treatment resistance in standard and high risk myeloma

  Study EGAS00001004558

• MT alignment

  Alignement including 83 MT AA sequences and 2 reference sequences, rCRS and RSRS

  Dataset EGAD00010001574

• STAT3 ChIPseq of PC-9 and KHM-3S with and without tarceva

  Dataset EGAD00001000844

• DAC - The Netherlands Cancer Institute - Antoni van Leeuwenhoek

  Dac EGAC00001003316

• THE NOWAC BLOOD-BREAST CANCER COMMITEE DATA ACCESS AGREEMENT

  Dac EGAC00001000743

• The admixture histories of Cabo Verde

  Dac EGAC00001002727

• UK Biobank Access - http://www.ukbiobank.ac.uk/using-the-resource/

  Dac EGAC00001000641

• TNBC (COH_TNBC_RNAseq) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002518

• TNBC (UW_OvCa_RNASeq) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002524

• TNBC (UW_OvCa_WGS) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002544

• Director of the Institute of Reproductive Genetics, Münster, Germany

  Dac EGAC00001002589

• TNBC (COH_WGS) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002574

• Data access commitee at the Molecular Exercise Physiology group

  Dac EGAC00001002606

• The Genomic Landscape of Prostate Cancer Brain Metastases

  Study EGAS00001004557

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

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

  Study EGAS00001000566

• BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins

  BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins

  Study EGAS00001001598

• Colon cancer amplicon targeted sequencing study contaning WBCs, primary tumor tissue and plasma samples

  This dataset consists of amplicon targeted NGS paired-end raw data (FASTQ R1 and R2) obtained from 148 colon cancer patients. Specifically, we have 148 primary tumor tissue samples, 148 white blood cell samples, and 118 plasma samples collected at baseline.

  Dataset EGAD50000000084

• RNA-sequencing

  Raw reads from RNA-sequencing of monocyte-derived macrophages from three individuals with heterozygous TET2 loss (Ly9, Ly11, Ly14) and two wild-type controls (Ly8 and an unrelated control). Libraries were prepared using ScriptSeq RNA-Seq Library Preparation Kit and Illumina sequenced with paired-end 75bp reads.

  Dataset EGAD00001004784

• EATL-II whole-exome sequencing profile

  Enteropathy-associated T-cell lymphoma (EATL), a rare and aggressive intestinal malignancy of intraepithelial T lymphocytes, comprises two disease variants (EATL-I and EATL-II) differing in clinical characteristics and pathological features. Here we report findings derived from whole exome sequencing of 15 EATL-II tumor-normal tissue pairs.

  Dataset EGAD00001002220

• Transcriptional and DNA binding profiling of CEBPE in REH acute lymphoblastic leukaemia cells using shRNA RNA-Seq and ChIP-Seq

  Dac EGAC00001000891

• MPN_Genomes_validation_and_interim_samples

  MPN genome variant validation and interrogation of interim timepoints.

  Study EGAS00001000766

• scMultiomics

  ARID1B+/+ (control) and ARID1B+/- human telencephalic organoids at D120

  Study EGAS50000000343

• scRNAseq

  ARID1B+/+ (control) and ARID1B+/- human telencephalic organoids at D120

  Study EGAS50000000344

• Evolution_of_the_cancer_epigenome_in_myeloproliferative_neoplasms_2

  Whole genome sequencing and bisulphite sequencing of haematopoietic colonies

  Study EGAS00001002372

• bfast CohortD OAPL

  ctDNA mutation calls (one mutation per sample per line) for BFAST Cohort D including mutation-level data like coding change, allele frequency, etc.

  Dataset EGAD50000000148

• AWI-GEN 2 Microbiome Dataset

  AWI-Gen Phase 2 Microbiome Project for 1820 samples.

  Dataset EGAD00001015449

• CCTG IND.231 WGS DNA Sequencing Data

  41 WGS DNA sequences from: Phase I trial of CX-5461, a first-in-class G-quadruplex stabilizer in patients with advanced solid tumors enriched for DNA-repair deficiencies (CCTG IND.231)

  Dataset EGAD00001008756

• ICGC PCAWG Dataset: OV-AU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: OV-AU.

  Dataset EGAD00001003416

• ICGC PCAWG Dataset: OV-AU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: OV-AU.

  Dataset EGAD00001003415

• ICGC PCAWG Dataset: PACA-AU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: PACA-AU.

  Dataset EGAD00001003411

• ICGC PCAWG Dataset: PACA-AU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: PACA-AU.

  Dataset EGAD00001003410

• BLUEPRINT September 2016, ChIP-Seq T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38

  ChIP-Seq data for 4 sample(s) T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38. 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001002952

• BLUEPRINT September 2016, ChIPmentation Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38

  ChIPmentation data for 2 sample(s) Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38. 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002946

• BLUEPRINT September 2016, ChIPmentation Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38

  ChIPmentation data for 2 sample(s) Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002944

• Harnessing transposons for drug resistance gene discovery in cancer

  This study involves a forward genetic screen to identify common insertion sites in drug resistant clones. We will be utilising piggybac transposon systems in order to generate multiple drug resistant clones in a range of human cancer cell lines.

  Dataset EGAD00001000980

• Gastric Cancer Genetic Analysis of Metastasis

  To identify candidate drivers involved in oncogenesis and tumor evolution, we conducted an extensive genome sequencing analysis of metastatic progression in diffuse gastric cancer. This involved a comparison between a primary tumor from a Hereditary Diffuse Gastric Cancer Syndrome proband and its subsequent recurrence as an ovarian metastasis.

  Study phs000795

• Development of Precision Neoadjuvant-Adjuvant Therapies

  In clinical trials assessing neoadjuvant androgen deprivation therapy plus next-generation androgen receptor axis inhibitors, a subset of patients fail to demonstrate a complete pathologic response following treatment and radical prostatectomy. We performed exome and transcriptome analyses on laser capture microdissected foci of residual tumor from these patients.

  Study phs001399

• Familial Exome Sequencing in Rare Pediatric Phenotypes

  To discover novel candidate genes associated with rare Mendelian phenotypes, we will conduct individual genomic and phenotypic characterization using genome-wide array, pedigree exome sequencing, candidate genotyping, and pertinent clinical testing to define phenotype. Pedigrees included in this submission will have a variety of clinical pathological phenotypes.

  Study phs000553

• Single-cell RNA-seq, single-cell TCR-seq, single-cell BCR-seq, and CITE-seq of B and T cells

  To describe human tonsillar CD4+ T cells, especially IL10+ Foxp3- follicular CD4+ T cells (Tfr1, T follicular regulatory type 1), human tonsillar CD4+ T cells were analyzed with single-cell RNA-seq, single-cell TCR-seq, single-cell ATAC-seq, and CITE-seq.

  Study JGAS000827

• Perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma: Primary phase 2 trial results with ctDNA residual disease analyses

  This data set includes sequence files from whole genome sequencing of tumor (n=28), normal (n=28), and blood (n=113) specimens from a phase 2 clinical trial of neoadjuvant nivolumab and nivolumab/ipilimumab in resectable diffuse pleural mesothelioma (NCT03918252).

  Study EGAS50000001195

• Spatiotemporal genomic architecture informs precision oncology in glioblsatoma

  We characterized genomic and expression profiles across 127 multi-sector or longitudinal specimens from 52 glioma patients. We showed that, while samples from nearby geographical location shared similar genomic alterations (clonal or subclonal) and expression signatures, multifocal tumors were seeded from individual clones.

  Study EGAS00001001880

• Whole exome sequencing of preneoplasia lung adenocarcinoma

  Multi-region exome sequencing of 271 pulmonary nodules and matched adjacent lung tissue including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=49), adenocarcinoma in situ (AIS, N=42), minimally invasive adenocarcinoma (MIA, N=37), invasive lung adenocarcinoma (ADC, N=57) and adjacent lung tissues (Normal, N=88).

  Study EGAS50000000270

• Clonal Evolution and Blastic Plasmacytoid Dendritic Cell Neoplasm - Two Cases

  Here we present two case studies of sequential whole exome sequencing (WES) in patients, who both developed BPDCN throughout their medical history but primarily presented with lymphoid cancers (clonally related ALK-negative anaplastic large-cell lymphoma (ALCL) and T-lymphoblastic lymphoma (T-LBL)) and whose bone marrow at remission exhibited a CMML phenotype, from which in both cases BPDCN clones arose that subsequently became treatment refractory.

  Study EGAS50000000214

• Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A

  We describe recurrent chromothripsis and structural variation of chromosome 21 in a subset of patients in blast phase of a myeloproliferative neoplasm (BP-MPN), which alongside other structural variants leads to amplification of a region of chromosome 21 in ~25% of patients (‘chr21amp’). Chr21amp BP-MPN has a particularly aggressive and treatment-resistant phenotype. Here we provide high-depth whole genome sequencing (WGS) in five chr21amp BP-MPN cases, to a median coverage of 81x [range 77-86] and purity 79% [range 58-88%].

  Study EGAS00001007483

• Somatic mutations in healthy and leukemic blood progenitors reveal evolutionary mechanisms underlying childhood leukemia and differential patient outcome

  Study EGAS00001004593

• Brain_Disease_Wellcome_Leap_Delta_Tissue_ATAC

  Single cell and spatial multi-omic atlas of glioblastoma

  Study EGAS00001008083