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• Effect of ETS2 modulation on chromatin accessibility and enhancer activity in primary human macrophages

  3 datasets included: - H3K27ac ChIP in ETS2-edited and unedited TPP macrophages from 3 biological replicates - H3K27ac ChIP in ETS2-overexpressing and control M0 (resting) macrophages from 3 biological replicates - ATAC-seq (deep sequencing) in ETS2-edited and unedited TPP macrophages from 3 biological replicates

  Dataset EGAD50000000154

• Single-cell RNA sequencing of chemotherapy-resistant muscle-invasive urothelial bladder cancer

  All single-cell mRNA sequencing data were acquired from a single patient (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib).

  Study EGAS00001004233

• AT2 COPD Methylomics

  We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung AT2 cells isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease

  Study EGAS00001007386

• Circulating tumor DNA in urine and plasma of glioma patients - sequencing data

  Dataset consisting of sequence data from 36 glioma patients. Data includes; -Whole exome sequencing of tumour tissue and matched germline -Shallow whole genome sequencing of urine cell-free DNA -Targeted capture sequencing of plasma and CSF cell-free DNA Additional sequencing data are provided from non-glioma and healthy controls

  Dataset EGAD00001006156

• scRNA-seq of first and second trimester human gonads - HUGODECA dataset

  Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-10551

  Dataset EGAD00001009386

• Single-cell T-cell receptor sequencing of intraepithelial CD8+ αβ T-cells in celiac disease

  Single-cell paired TCR sequencing of intraepithelial CD8+ αβ T-cells in gluten-free diet treated and untreated celiac disease patients and in controls. (Paired end, amplicon sequencing).

  Study EGAS00001004989

• A108846B

  Whole genome sequencing for single cells for library A108846B 1636 cells; filetype=bam

  Dataset EGAD00001007092

• A90679

  Whole genome sequencing for single cells for library A90679 1034 samples; filetype=bam

  Dataset EGAD00001008219

• A95635B

  Whole genome sequencing for single cells for library A95635B 593 samples; filetype=bam

  Dataset EGAD00001008223

• A95635D

  Whole genome sequencing for single cells for library A95635D 367 samples; filetype=bam

  Dataset EGAD00001008224

• A95654A

  Whole genome sequencing for single cells for library A95654A 901 samples; filetype=bam

  Dataset EGAD00001008225

• A95662A

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

  Dataset EGAD00001008226

• A95664B

  Whole genome sequencing for single cells for library A95664B 630 samples; filetype=bam

  Dataset EGAD00001008227

• Adaptive long-read and transcriptome sequencing detail a submicroscopic inv(15)(q14q15), generating two fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency

  Study an inversion affecting MEIS2 using ONT adaptive sequencing.

  Study EGAS50000000632

• Prostate cancer datasets RNA Seq

  Total RNA Seq: 15 Samples (2 patients (MF1 and MF3)) (HiSeq) and Poly A RNA Seq: 27 Samples (4 patients Normal and Tumour ) (HiSeq)

  Dataset EGAD00001004468

• Exome sequencing to evaluate HER2/ERBB2 mutations in cancer

  ERBB2/HER2 transmembrane and juxtamembrane domain mutations in cancer. Exome sequencing of tumor and matched blood and 2 blood samples from relatives.

  Dataset EGAD00001004351

• WGS and ONT Bams Accompanying Loose Ends Dataset

  Short read whole genome and long read Oxford Nanopore sequencing of matched tumor/normal material from 10 Melanoma and 1 case of TNBC.

  Dataset EGAD00001011047

• 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

• Patient-Derived Follicular Lymphoma Spheroids recapitulate lymph node signaling and immune profile, uncovering galectin-9 as a novel immunotherapeutic target

  RNA-seq data from CD20+ sorted cells obtained from peripheral blood and lymph node Follicular Lymphoma patients. These samples were unstimulated after thawing and additionally, peripheral blood samples were stimulated during 7 days in culture as described in Dobaño-López C et. al.)

  Study EGAS50000000233

• Smart-seq3 scRNA-seq of cells from primary (OV2295) and metastatic (OV2295R2) high-grade serous ovarian cancer cell-line

  In this project, single cells extracted from two high-grade serous ovarian cancer cell-lines, one primary (OV2295) and one metastatic (OV2295R2), where split into two 384 well plates and libraries were prepared using Smart-seq3 single cell RNA sequencing (Hagemann-Jensen et al, 2020).

  Study EGAS00001006868

• WES and RNA-seq data of 11 cancer patients with multiple cancer types

  This dataset includes WES and RNAseq from 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy samples, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems. Paired-end reads are provided in fastq format.

  Dataset EGAD00001010169

• RNA Sequencing of Control and Myotonic Dystrophy Type 1 Cells During Myogenic Differentiation

  RNAseq data of 30 muscle cell samples (proliferating myoblasts to differentiating myotubes) of immortalized control cells, and myotonic dystrophy type 1 (DM1) patient-derived cells and their edited versions.

  Dac EGAC50000000592

• Exome and RNA sequencing of Greenlanders

  This study contains whole exome sequence of 27 Greenlanders and deep RNA sequencing of 17 Greenlanders

  Study EGAS00001002727

• RNAseq cutaneous and uveal melanoma liver metastases

  RNA sequencing analyses of tumor liver metastases from untreated cutaneous melanoma (CM) and uveal melanoma (UM) patients.

  Study EGAS00001004794

• Delineating intratumoural heterogeneity and neoantigen-directed immune escape in Esophageal Squamous Cell Carcinoma

  Delineating intratumoural heterogeneity and neoantigen-directed immune escape in Esophageal Squamous Cell Carcinoma

  Study EGAS00001003832

• RNA sequencing of human ILC3 from lymphoid organs and blood

  Rna sequencing of purified human group 3 innate lymphoid cells from non-reactive lymph nodes and spleen, inflamed tonsils and peripheral blood.

  Dataset EGAD00001003704

• Gastric Cancer Organoid Cultures and Tumors RNASeq Data

  RNASeq data generated from organoid cultures established from gastric cancers and normal mucosae, paired tumor frozen tissues, and cultured fibroblast.

  Dataset EGAD00001004302

• Single cell sequencing of newly-diagnosed and recurrent GBM

  Single cell RNA and CITE sequencing of newly-diagnosed and recurrent GBM

  Dataset EGAD00001006778

• 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-Seq profiles from the CheckMate-649 Clinical Trial

  This dataset contains RNA sequencing (RNAseq) data of 814 patients from the CheckMate 649 clinical trial whose ICF allows data deposition into a public repository. Gene expression profiling was performed retrospectively using RNAseq on a subset of baseline tumor samples. Paired-end FASTQ files were processed on Seven Bridges platform (Seven Bridges Genomics).

  Dataset EGAD50000001105

• Pediatric CNS tumor classification by DNA-methylation dataset

  In this study nanopore sequencing was applied to obtain sparse DNA methylation profiles from pediatric CNS tumor samples. A neural network was used to classify the tumor based on the obtained methylation profile.

  Dataset EGAD00010002599

• 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

• Ultra-fast deep-learned pediatric CNS tumor classification.

  In this study nanopore sequencing was applied to obtain sparse DNA methylation profiles from pediatric CNS tumor samples. A neural network was used to classify the tumor based on the obtained methylation profile.

  Dataset EGAD00001011303

• 419 Japanese healthy control

  Genotypes of 419 Japanese healthy individuals genotyped by using of SNP arrays (Genome-Wide Human SNP Array 6.0 and Axiom Genome-Wide ASI 1 Array). CEL files and CHP files are included in this data set.

  Study JGAS000120

• Global RNA sequencing data of human iPSC-derived microglia from frontotemporal dementia (FTD) patients

  Global RNA sequencing was performed in RNA samples extracted from human iPSC-derived microglia from healthy controls and sporadic (non-genetic) and genetic C9orf72 hexanucleotide repeat expansion-carrying patients with FTD.

  Study EGAS50000001688

• Genome sequencing of oesophagus atresia families

  To gain insight into gene variants and genes associated with isolated Oesophageal atresia (OA) we conducted whole genome sequencing on samples from three families with recurrent cases affected by congenital and isolated tracheoesophageal fistula (TEF).

  Study EGAS00001004394

• Discovery of cancer prognostic markers based on comparison of gene expression in colorectal cancer samples.

  Here, we analyse bulk mRNA-seq data derived from normal tissues adjacent to tumors (NATs) and tumour tissues of colorectal cancer (CRC), including 80 NAT samples and 80 tumour samples.

  Study EGAS00001005068

• Genomic and transcriptomic profiling of carcinogenesis in patients with familial adenomatous polyposis

  Whole-exome sequencing (WES) and whole-genome sequencing (WGS) were performed on matched adjacent normal tissues, multiregionally sampled adenomas at different stages and carcinomas from 5 patients with FAP and 1 patient with MUTYH-associated polyposis (MAP) (n=56 exomes; n=56 genomes; n=8,757 single cells).

  Dataset EGAD00001005457

• Predictive value of genomic, transcriptomic and epigenetic biomarkers in patients with recurrent and/or metastatic HNSC treated with PD-1/PD-L1 inhibitors

  Immune checkpoint inhibitors have improved survival in several solid tumors, including head and neck squamous cell carcinoma (HNSCC). However, current use of PD-1/PD-L1 inhibitors relies on PD-L1 expression, which does not reliably predict patient response. Therefore, better predictive biomarkers are needed to identify which patients benefit from immunotherapy. Previous studies suggest that genomic and transcriptomic features may help predict treatment response. This study aims to integrate genomic, transcriptomic, and methylomic data from 31 patients with recurrent/metastatic HNSCC to identify new biomarkers of resistance to anti-PD-1/PD-L1 therapy.

  Study EGAS50000001746

• 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

• Genetic Variation and Signatures of Natural Selection in Diverse Africans

  Our study identified candidate regions of genome involved in adaptation and identified regions associated with selected phenotypes.

  Study phs000449

• COVID-19 progression and convalescence in common variable immunodeficiency patients

  Longitudinal analysis of single-cell RNAseq datasets of PBMCs from COVID-19 CVID patients and controls.

  Study EGAS50000000368

• Macrophage polarisation to M1 and M2 phenotypes

  iPSC-derived macrophages were polarised with LPS/IFN-gamma or IL4 to M1 and M2 phenotypes, respectively.

  Study EGAS50000000820

• Ion Proton WES raw and processed data from and novel immunodeficiency proband.

  BAM and VCF files from WES of an affected proband with a novel immunodeficiency phenotype caused by homozygous mutation of SLC19A1.

  Dataset EGAD50000000524

• WES cutaneous and uveal melanoma liver metastases

  Whole exome sequencing analyses of tumor liver metastases from untreated cutaneous melanoma (CM) and uveal melanoma (UM) patients.

  Study EGAS00001004795

• Whole exome and transcriptome sequencing of gastric cancer patients

  Whole exome and RNA-seq of matched normal gastric mucosa (n=34) and gastric cancer tissues (n=34) from gastric cancer patients (n=34)

  Dataset EGAD00001004164

• Clinical and genetic factors associated with tumor response to neoadjuvant (chemo)radiotherapy, survival and recurrence risk in rectal cancer

  Dataset consists of 216 samples, with each sample having a BAM, BAI and VCF file.

  Dataset EGAD00001011297

• single-cell RNA-sequencing of human/mouse colonic crypts

  Human colonic stem cells are slow cycling compared with murine rapid cycling stem cells. Our study aims to identify slow cycling stem cell in human normal colon in vivo and to analyze gene signatures among rapid cycling stem cells, slow cycling stem cells and secretory progenitor cells using single cell RNA-seqencing . We further investigated in vivo dynamics of human colonic stem cell using patient-derived gene-enginered organoids and orthotopic xenotransplantation.

  Study JGAS000550

• In this study, we performed exon sequencing (WXS) of 80 paired Brain cancer tumors and adjacent normal tissues to identify novel potential biomarkers. We extracted mutational signatures which induce somatic mutations . Our study covers a comprehensive genetic framework that can be used in clinical trials and treatment modalities in Brain cancer.

  In this study, we performed exon sequencing (WXS) of 80 paired Brain cancer tumors and adjacent normal tissues to identify novel potential biomarkers. We extracted mutational signatures which induce somatic mutations . Our study covers a comprehensive genetic framework that can be used in clinical trials and treatment modalities in Brain cancer.

  Study EGAS00001002352

• Major Depression: Stage 1 Genomewide Association in Population-Based Samples

  Identification of genomic regions that confer susceptibility to or protection from major depressive disorder (MDD) via genomewide association. Consent groups and participant set Psychiatric and Related Somatic Conditions (PRSC): 3741 (1821 cases, 1822 controls, 98 others)

  Study phs000020

• ICARUS-LUNG01-ExomeSeq

  Whole exome sequencing (WES) on frozen tumor biopsies at BL to identify genomic alterations associated with response/resistance. Non- synonymous point mutations, indels, homozygous deletions, loss of heterozygosity (LOH) and low, medium, and high-level amplifications were assessed.

  Study EGAS50000000733

• WGS bam

  We established 21 patient-derived pHGG orthotopic xenograft (PDOX) models and eight matched cell lines from diverse groups of pHGG. Here are all available Whole Genome Sequencing (WGS) data from patient tumor, PDOX, and cell lines from our study.

  Study EGAS00001005159

• WES bam

  We established 21 patient-derived pHGG orthotopic xenograft (PDOX) models and eight matched cell lines from diverse groups of pHGG. Here are all available Whole Exome Sequencing (WES) data from patient tumor, PDOX, and cell lines from our study.

  Study EGAS00001005160

• NLG-LBC-05 ctDNA

  Correlative analysis of circulating tumor DNA (ctDNA) in aggressive large B-cell lymphoma patients treated in NLG-LBC-05 phase II trial. Whole genome and targeted sequencing was applied to longitudinal plasma cell-free DNA and diagnostic tumor tissues.

  Study EGAS00001005835

• Sequence-based gene expression in uterine and ovarian carcinosarcomas

  Gynecologic carcinosarcomas (CS), including more generally uterine (endometrial) and less frequently ovarian localization, are histologically defined as biphasic neoplasms composed of carcinomatous (C) epithelial and sarcomatous (S) malignant components. We report a comprehensive analysis of 20 patients of macro-dissected samples of C and S components through RNA sequencing.

  Dataset EGAD00001009099

• RNA sequecing of primary B cells infected with Epstein-Barr virus (EBV) or stimulated with heat-inactivated EBV

  Naïve (CD27-IgD+) B cells were isolated from buffy coat preparations of healthy donors using CD19 magnetic beads, followed by reals of CD19 beads and incubation with IgD-biotin and anti-biotin magnetic beads. B cells were infected with EBV by spinoculation or stimulated with heat-inactivated EBV and control cells were left uninfected. RNA was extracted immediately after isolation in un-infected B cells. From EBV-infected B cells and B cells stimulated with heat-inactivated virus, RNA was extracted 24 and 96 hours after infection / stimulation.

  Dataset EGAD50000000305

• A genome-wide meta analysis on stroke and ischemic stroke within four populations

  In this analysis a genome-wide meta-analysis was performed on all stroke and ischemic stroke.

  Study EGAS00000000060

• RNA sequencing data of child-mother pairs, maternal smoking.

  RNA sequencing data of whole blood samples from smoking and non-smoking mothers and their children at gestation/birth and follow-up years.

  Dataset EGAD00001002011

• Whole genome and whole exome sequencing of mucosal melanomas

  NGS of 10 mucosal melanomas:Whole genome sequencing of 5 mucosal melanomas and matched normal DNAWhole exome sequencing of 5 mucosal melanomas and matched normal DNA

  Dataset EGAD00001000945

• 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

• Genomic characterization of NUT midline carcinoma

  In this study, we sequenced two NUT midline carcinoma genomes. Analysis of rearrangement breakpoint provided information on the generating event of BRD-NUT rearrangements. Mutational signature analysis also revealed biological process during tumorigenesis of NUT midline carcinomas.

  Study EGAS00001001934

• ChIP-seq data of Hodgkin lymphoma cell line L-428

  ChIP-seq data (H3K4Me3, H3K27Ac histone modifications) of Hodgkin lymphoma cell line L-428. Samples were processed as previously described (Sud et al., 2018). The files are in bam format, aligned to build 37.

  Study EGAS00001003033

• BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia

  Hijacking of primitive hematopoietic enhancers, or generation of a neo-enhancer by genomic amplification, results in deregulation of BCL11B as the defining feature of a subset of T/myeloid leukemia

  Study EGAS00001004810

• RNA Sequencing of Colorectal Liver Metastases

  Reverse-stranded paired-end 75 base-pair RNA sequencing libraries of 93 metastatic FFPE samples were constructed using Illumina Total RNA Stranded Kits. Ribosomal RNAs (rRNAs) were depleted by using the Ribo-Zero rRNA Removal Kit (Illumina). Libraries were sequenced on a HiSEQ2500 machine. Five samples were re-sequenced using paired-end 50 base-pair libraries due to the smaller insert sizes.

  Dataset EGAD00001004111

• Molecular programs of melanoma brain metastases (MBM)

  We performed paired-end whole transcriptome sequencing of fresh frozen or intraoperative brain metastases of therapeutically treated stage IV melanoma patients. In addition, we analysed the epigenetic landscape of tumors usind Illumina 850k bead chip technology.

  Study EGAS00001005976

• RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Dataset EGAD00001001944

• EGAD00010000736

  AAD case and control samples from UK and Norway

  Dataset EGAD00010000736

• Analysis of cell type contributions to cell free DNA in health and disease.

  This study looks at cell type contributions to cell free DNA in health and disease.

  Study EGAS50000000178

• GBM Up and Down Responder EZH2 ChIPseq

  ChIPseq using anti-EZH2 with a sheared input DNA control to assess EZH2 genomic biding in one longitudinal pair of samples (pre- and post-treatment) from one UP and one DOWN responder GBM patient

  Dataset EGAD50000000134

• Whole exome-sequencing of pediatric and adult H3-K27M diffuse midline glioma

  H3-K27M mutant difffuse midline gliomas across different age groups and anatomical locations were profiled by WES.

  Study EGAS00001006431