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• NIDDK IBD Genetics Consortium Repository Exome Chip

  The Illumina Infinium HumanExome+ BeadChip contains putative functional exonic variants selected from individual exome and whole-genome sequences from diverse populations. It includes nonsynonymous variants, splice variants and stop-altering variants. It also includes tags for previous GWAS-identified loci, ancestry informative markers, markers designed for identity by descent analyses, synonymous variants, fingerprint SNPs common to major genotyping platforms, mitochondrial SNPs, chromosome Y SNPs, and HLA tag SNPs. For more information as well as a detailed description of the variant calling and QC procedures, see Li et al. (2016). Li, D., et al. (2016) A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition. Gastroenterology, 151, 1-9. PMID: 27492617.

  Study phs001723

• TRACERx NSCLC - whole genome sequencing for ctDNA study

  Data used in "An ultra-sensitive and specific ctDNA assay provides novel pre-operative disease stratification in early stage lung adenocarcinoma"

  Dataset EGAD50000000452

• HiSeq Colorectal Cancer Dataset

  Set of 19 patients afflicted with colorectal cancer with matching preoperative and postoperative blood plasma, PBMC, and tumor biopsy sequencing data. Originally referenced by Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. Nat Med. 2020, Zviran et. al.

  Dataset EGAD00001011186

• Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform

  Ultra low coverage sequencing results from the project 'Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform'. Sequencing data of sample NA12877 and NA12878 generated from 3 nanopore sequencing runs are included in this dataset.

  Dataset EGAD00001004052

• Prostate cancer datasets WGS

  Low pass WGS: 48 samples (5 blood samples from 6 patient data): 22 Tumour cores and 26 normal/benign cores (Next Seq )

  Dataset EGAD00001004466

• Exome-sequencing of human B cell lymphoma cell lines

  26 cell lines derived from human Diffuse Large B Cell lymphomas (DLBCL) or Burkit Lymphomas (BL) were subjected to whole exome sequencing. Exome capture was carried out using the SeqCap EZ Exome Library 2.0 kit (Roche/Nimblegen) and 100 bp single-read sequencing was performed on a HiSeq2500 (Illumina). 82% of the coding region was covered at least 30x.

  Study EGAS00001001463

• The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways

  A comprehensive constellation of somatic non-silent mutations and copy number (CN) variations in ocular adnexa marginal zone lymphoma (OAMZL) is unknown. By utilizing whole-exome sequencing in 69 tumors we define the genetic landscape of OAMZL. Mutations and CN changes in CABIN1 (30%), RHOA (26%), TBL1XR1 (22%), and CREBBP (17%) and inactivation of TNFAIP3 (26%) were among the most common aberrations. Candidate cancer driver genes cluster in the B-cell receptor (BCR), NFkB, NOTCH and NFAT signaling pathways. One of the most commonly altered genes is CABIN1, a calcineurin inhibitor acting as a negative regulator of the NFAT and MEF2B transcriptional activity. CABIN1 deletions enhance BCR-stimulated NFAT and MEF2B transcriptional activity, while CABIN1 mutations enhance only MEF2B transcriptional activity by impairing binding of mSin3a to CABIN1. Our data provide an unbiased identification of genetically altered genes that may play a role in the molecular pathogenesis of OAMZL and serve as therapeutic targets.

  Study EGAS00001006631

• Transcriptomic profiling of patient-derived xenografts and organoids in prostate cancer

  Dataset contains RNA-seq of 30 samples (normal prostate tissue, human prostate cancer, PDX and organoids).

  Dataset EGAD00001006404

• Clonal_expansion_of_mutated_cell_population_in_bladder_urothelium_

  1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference.

  Study EGAS00001001687

• Paired exome analysis in urothelial carcinoma

  In this study we characterized genomic alterations in two to five metachronous tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth), Ultra deep targeted sequencing (~6,809x mean read depth) and whole transcriptome RNA-seq was performed for all samples. In addition multiregional WES was performed on 8 adjacent regions from a single tumor.

  Study EGAS00001001686

• Tissue DNA, WBC DNA and cfDNA (deep-)sequencing of mCRC patients treated with doublet chemotherapy and anti-EGFR in the CAIRO5 study

  This study assessed whether ctDNA based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC) derived DNA. In total, 183 cfDNA and 49 WBC samples, along with 28 tissue samples, from 52 metastatic colorectal cancer patients participating in the prospective phase III CAIRO5 clinical trial (NCT02162563) were analyzed using the PGDx elio plasma resolve assay.

  Study EGAS00001006695

• Ultra-long whole-genome and Cas9-targeted nanopore sequencing of fibroblasts: FSHD, BAMS, healthy controls

  Data from the D4Z4End2End study (Xiao et al. 2025), for genetic and epigenetic analysis of the D4Z4 macrosatellite in health and disease.

  Dataset EGAD50000001551

• Deep-Seq: Resistance to anti-EGFR therapy in colorectal cancer

  In this study we performed ultra deep sequencing of genes associated with anti-EGFR resistance, such as KRAS, BRAF, PIK3CA, and EGFR in 17 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy.

  Dataset EGAD00001000688

• Single-Cell TCR/BCR Sequencing for Korean COVID-19 Vaccinated and Patient Samples

  We conducted longitudinal single-cell TCR/BCR sequencing for COVID-19 vaccinated cases (297 samples from 112 cases) and COVID-19 infected cases classified as Asymptomatic (26 samples from 12 cases), Mild (82 samples from 37 cases), Moderate (123 samples from 50 cases), Severe (216 samples from 58 cases), and Critical (142 samples from 41 cases) according to the NIH guideline.

  Study phs003341

• Molecular Characterization of Prostate Cancer Specimens by Bulk and Single Cell Analysis

  Version 1: We performed single-cell RNA-sequencing (scRNA-seq) of fresh biopsies from metastatic castration resistant prostate cancer. Additionally, where available, we performed matched bulk whole exome sequencing (WXS; tumor and normal paired) and whole transcriptome sequencing for the same individuals. We also performed bulk whole exome (WXS) and RNA-sequencing (RNA-Seq) from FFPE pre-treatment biopsies from patients with clinically localized high-risk prostate cancer.Version 2: We added data from a randomized phase 2 trial of radium-223 with or without pembrolizumab in patients with Metastatic Castration-Resistant Prostate Cancer (mCRPC) to bone. After enrollment, study participants underwent bone biopsy and were randomized 2:1 to receive radium-223 at 55 kBq/kg every 4 weeks + pembrolizumab at 200 mg every 3 weeks (Arm A, R223+P) or radium-223 at 55 kBq/kg every 4 weeks alone (Arm B, R223). Stratification factors were alkaline phosphatase ≥220 vs. Data generated includes bulk whole exome sequencing (WXS), ultra-low pass whole genome sequencing (WGS) at 0.1X coverage, and targeted-capture sequencing. The ultra-low pass sequencing was used as part of the selection criteria for the target capture sequencing. Note: Two subjects in this study are linked to phs001577 and phs000915 respectively.

  Study phs001988

• WES, ultra-deep sequencing exome and RNAseq data of diseased liver samples

  1. Utra-deep exome sequencing data, illumina pair-end reads, fastq, 190 samples 2. WES data, illumina pair-end reads, fastq, 120 samples 3. RNA-seq data, illumina, pair-end reads, fastq, 20 samples

  Dataset EGAD00001004792

• Single-Cell DNA Methylation Profiling via scTAMseq

  This dataset comprises single-cell DNA methylation and nuclear genotyping profiles of 7 total bone marrow aspirates (donors A.1-A.7) and 5 CD34+-enriched bone marrow samples (donors B.1-B.5) generated using the scTAMseq protocol. Sequencing was performed on the Mission Bio Tapestri platform, targeting a panel of 448 CpGs to assess epigenetic patterns and We also included 147 genomic regions commonly mutated in clonal hematopoiesis and 20 regions targeting chromosome Y. Samples B.1 & B.5, B.2 & B.4 and A.2 & A.5 were, in pairs, multiplexed into single tapestri lanes.

  Dataset EGAD00001015498

• Whole Genome Sequences of 18th century African descended individuals from Charleston, South Carolina.

  This study presents Whole Genome Sequencing results from the Anson Street African Burial Ground Project, which is a community-based initiative aimed at understanding the histories of 37 Ancestors found during construction in Charleston, South Carolina. Here we report fastq files for all 37 Ancestors. DNA was extracted at the University of Tennessee-Knoxville following Dabney et al. 2013, and dual index libraries prepared using a modified NEBNext Ultra II kit with partial USER enzyme digestion. Libraries were then enriched for human genomic DNA (MyBaits) and sequenced on Illumina Platforms.

  Study EGAS00001006693

• WES dataset of a TIL-ACT metastatic melanoma cohort

  Whole-exome sequencing (WES) data from 13 patients with metastatic melanoma in a TIL-ACT cohort, generated to characterize tumor genomics and neoantigen landscapes relevant to adoptive T cell therapy.

  Dataset EGAD50000001731

• Analysis of the co-occurrence of LOY and CHIP in Alzheimer's disease patients and control individuals using whole-exome sequencing (WES)

  We performed deep whole-exome sequencing of FACS-isolated CD4+ T lymphocytes, NK and myeloid cells from men with AD and controls exhibiting either LOY or retention of Y chromosome (ROY). We found 39 sequence variants in known (canonical) myeloid driver genes of clonal hematopoiesis (MD-CH) and known lymphoid driver genes (LD-CH), and maximally 14 (35%) of these could co-exist with LOY within the same clone. We further describe 192 unknown drivers of clonal hematopoiesis (UD-CH), which were markedly enriched in AD-LOY individuals (odds ratio=4.8, Benjamini-Hochberg-adjusted p=0.041), and over 20% of these variants were protein-truncating. In myeloid cells, the total burden of all detected drivers correlated with the percentage of LOY cells (Spearman ρ=0.52, adjusted p=0.00041).

  Study EGAS00001008234

• RNA-Seq data of S24 cells for the publication Recording physiological history of cells with chemical labeling.

  Recordings of elevated calcium levels allowed selections of cells from heterogenous populations for transcriptomic analysis. Paired RNA-Seq from S24 cells using Takara SMARTer Ultra Low Input RNA v4 kit and sequencing on a Illumina NovaSeq 6000.

  Dataset EGAD50000000082

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer - DEDICATION co-hort

  Liquid biopsies generated for minimal residual disease monitoring of non-small cell lung cancer. Ultra deep targeted sequencing of lung cancer related genes with UMIs. This dataset contains the dedication cohort

  Dataset EGAD50000002230

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer - Biobank co-hort

  Liquid biopsies generated for minimal residual disease monitoring of advanced non-small cell lung cancer. Ultra deep targeted sequencing of lung cancer specific genes, with UMIs. This dataset consists of the biobank cohort

  Dataset EGAD50000002231

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• High-depth whole genome sequencing of paired ductal carcinoma in-situ (DCIS) and germline control samples from 26 individuals.

  Deposited here are whole-genome sequencing data for 26 paired breast cancer DCIS and matched-normal samples taken from the same individual. Average sequence coverage is 118x for DCIS samples and 41x for matched-normals. Matched-normal samples are from blood. Sequencing was performed on an Illumina HiseqX. Due to specific restrictions imposed by the ethical approval at sample collection, the use of the germline data is restricted to filtering of somatic mutation calls only and cannot be used outside this purpose.They are a part of a broader project that uses high-depth WGS to investigate the somatic mutation genomic landscape of DCIS in order to uncover biological insights into breast cancer progression as well as possible methods to stratify DCIS patients for individualised therapy or disease monitoring.

  Dataset EGAD50000002237

• RNA-Sequencing and Somatic Mutation Status of Adrenocortical Tumors: Novel Pathogenetic Insights

  To investigate the relationship between transcriptome profile and genetic background in a large series of adrenocortical tumors and to identify new potential pathogenetic mechanisms, we performed transcriptome profiling by high-throughput sequencing. We collected snap-frozen tissue from patients with adrenocortical tumors (n = 59) with known genetic background: 26 adenomas with Cushing syndrome, 17 adenomas with mild autonomous cortisol secretion, 9 endocrine-inactive adenomas, 7 adrenocortical carcinomas. Additionally, we sequenced 4 control samples.

  Study EGAS00001004533

• Breast Cancer Single-Cell RNA-Seq Dataset

  Single-cell RNA-Sequencing of 26 primary breast cancers from Wu et al. (2021) study. Data was generated using the Chromium controller (10X Genomics) and sequenced on the NextSeq 500 platform.

  Dataset EGAD00001007495

• Ultra-sensitive ctDNA monitoring required for predicting response and resistance to immunotherapy in advanced melanoma

  Circulating tumor DNA (ctDNA) monitoring in peripheral blood has shown promise for disease surveillance and prognostication of ICI response. Yet even in the metastatic context, ctDNA signals can be missed, suggesting the need for increased assay sensitivity. We used a tumor-informed ctDNA assay capable of detection down to 1 part-per-million (PPM) ctDNA to profile 188 plasma samples from 23 melanoma patients receiving ICI over several years. Residual disease was detected in ctDNA over a broad range, from 130,000 PPM down to 2.3 PPM, with approximately a quarter of detections below 50 PPM. Early on-treatment increases in ctDNA level, and both ctDNA-based molecular clearance (mCR) and molecular progression (mPD) were all prognostic of both OS and PFS. Additionally, mCR consistently preceded radiographic imaging. Our results show the importance and utility of an ultra-sensitive ctDNA assay in advanced melanoma treated by ICI with potential implications for other cancers.

  Study EGAS50000000550

• Whole-exome ultra-high throughput sequencing in brain samples of suicide victims who had suffered from major depressive disorder and control subjects who had died from other causes

  We carried out whole-exome ultra-high throughput sequencing in brain samples of suicide victims who had suffered from major depressive disorder and control subjects who had died from other causes. This study aimed to reveal the selective accumulation of rare variants in the coding and the UTR sequences within the genes of suicide victims. We also analysed the potential effect of STR and CNV variations, as well as the infection of the brain with neurovirulent viruses in this behavioural disorder. As a result, we have identified several candidate genes, among others three calcium channel genes that may potentially contribute to completed suicide. We also explored the potential implication of the TGF-β signalling pathway in the pathogenesis of suicidal behaviour. To our best knowledge, this is the first study that uses whole-exome sequencing for the investigation of suicide.

  Study EGAS00001002818

• Whole-exome ultra-high throughput sequencing in brain samples of suicide victims who had suffered from major depressive disorder and control subjects who had died from other causes.

  We carried out whole-exome ultra-high throughput sequencing in brain samples of suicide victims who had suffered from major depressive disorder and control subjects who had died from other causes. This study aimed to reveal the selective accumulation of rare variants in the coding and the UTR sequences within the genes of suicide victims. We also analysed the potential effect of STR and CNV variations, as well as the infection of the brain with neurovirulent viruses in this behavioural disorder. As a result, we have identified several candidate genes, among others three calcium channel genes that may potentially contribute to completed suicide. We also explored the potential implication of the TGF-β signalling pathway in the pathogenesis of suicidal behaviour. To our best knowledge, this is the first study that uses whole-exome sequencing for the investigation of suicide.

  Study EGAS00001003081

• WGS datasets of pediatric glioblastoma

  WGS with linked reads of pediatric glioblastoma. For each patient, blood and tumor tissue were sequenced. For two patients, we also provide sequencing data for the blood of their parents.

  Dataset EGAD00001005212

• DIPG WES and RNA-Seq

  We characterised H3K27M-mutant diffuse intrinsic pontine glioma (DIPG, n=21) and RNA-Seq (n=26 DIPG, 12 normal brain)

  Dataset EGAD00001006450

• Scalable ultra-high-throughput multiplexed single-cell chromatin and RNA profiling reveals gene regulatory dynamics during stimulation time courses and CRISPR perturbation screens

  Data for 1) hiPSC-derived macrophages across a polarization time course from the naive M0-state to the M1- and M2-states, 2) Primary T-cells differentiated to helper subtypes, and 3) spontaneous differentiation of hiPSCs upon perturbation of GATA2, NR4A2 or SOX17

  Dac EGAC50000000485

• Whole genome sequencing data of pediatric hypodiploid B cell acute lymphoblastic leukemia

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) bone marrow samples of one hypodiploid ALL patient (ALLT-351). Sequencing library was made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001856

• RNA sequencing

  RNAseq of 45 high-grade serous ovarian cancer tumour samples. Libraries were generated using the NEB Ultra II Directional RNA library Prep kit with polyA enrichment. Libraries were sequenced as paired-end 50 or 100bp on an Illumina NextSeq or NovaSeq.

  Dataset EGAD00001009844

• WES of melanoma tumours prior to combined immune checkpoint blockade treatment.

  Paired melanoma tumor and normal (PBMC) WES data from a cohort of 26 patients subsequently treated with combined immune checkpoint blockade.

  Dataset EGAD00001005941

• RNA-seq and scRNA/TCR-seq data for publication: "Pharmacological inhibition of nonsense-mediated mRNA decay enhances anti-tumour immunity"

  PDFs RNA-seq and scRNA/TCR-seq data for Pharmacologic inhibition of nonsense-mediated mRNA decay enhances anti-tumour immunity

  Dataset EGAD50000001720

• Studies in the Pathogenesis of Systemic Capillary Leak Syndrome (SCLS, Clarkson Disease)

  Systemic capillary leak syndrome (Clarkson disease) is an ultra-rare disease of unknown etiology. Patients experienced transient and recurrent episodes of hypotensive shock and massive peripheral edema due to plasma extravasation, often precipitated by minor viral infections. Disease onset occurs most frequently in middle age, and there is no family history. More than 90% of patients with the disease have monoclonal gammopathy of unknown significance (MGUS). The goal of the study is to determine pathogenic mechanisms and identify genetic underpinnings of the disease. Toward this end, we performed whole genome sequencing (WGS).

  Study phs003261

• Mutation signatures in melanocytic nevi reveal characteristics of defective DNA repair

  Nevi are common benign melanocytic neoplasms that can be found on any skin location and share many of the genomic hallmarks of melanoma. In our recent report involving whole-exome sequencing of acquired nevi (Stark et al., 2018), ultra-violet radiation (UVR) related somatic mutation signatures (“signature 7”) (Alexandrov et al., 2013) were frequently observed in all lesions that were located on sun-exposed sites. In the study presented herein, we sought to investigate whether an independent Spanish cohort (Valencia, Spain) of minimally sun exposed nevi had genomic features consistent with our previous findings.

  Study EGAS00001004274

• Whole blood RNA sequencing of individuals from Nepal

  This study utilized blood samples collected in Lalitpur, Nepal as part of the Strategic Typhoid Alliance across Africa and Asia (STRATAA) study. The dataset comprises whole blood RNAseq of 376 febrile individuals from Nepal. Blood was collected in PAXgene tubes and sent to Monash University (Melbourne, Australia) where RNA was extracted using the PAXgene Blood RNA kit before being sent to the Wellcome Sanger Institute (Hinxton, UK) for sequencing. Library prep used NEBNext Ultra II RNA custom kits on an Agilent Bravo WS automation platform with poly(A) pulldown. After PCR, plates were purified using Agencourt AMPure XP SPRI beads and libraries were quantified using Biotium Accuclear Ultra high sensitivity dsDNA Quantitative kits. Pooled libraries were normalised to 2.8 nM. Samples were globin depleted using KAPA RNA HyperPrep with RiboErase. Libraries were then subjected to 2x100bp paired-end sequencing on Illumina NovaSeq. Each library was sequenced to an average of 80 million reads. The STRATAA study was approved by the Nepal Health Research Council (NHRC, ref 283 306/2015) and OxTREC (Oxford Tropical Research Ethics Committee, ref 39-15). All participants provided informed consent for human genetic tests.

  Dataset EGAD00001011131

• Duplex sequencing of 26 genes

  Buccal samples and paired esophageal epithelium were obtained using the three sizes of swabs and endoscopic biopsy, respectively. Forty samples from 10 subjects were analyzed via duplex sequencing. This dataset contains bam files that were mapped to the GRCh37 reference genome.

  Dataset EGAD50000000998

• RNA-seq samples

  Raw FASTQ files obtained by RNA sequencing of tumor samples from patients (age 12-29) with newly diagnosed, recurrent intermediate or high-grade sarcoma.

  Dataset EGAD00001008393

• Somatic mutations in twin breast cancers (2019-04-03)

  The aim of this study is to investigate the somatic mutations in twins with BRCA1/2 negative breast cancer with no strong family history. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004890

• shallow whole genome sequencing BAM files aligned to the human reference genome GRCh38

  We profiled large B-cell lymphoma (LBCL) patient plasma samples with ultra-low-pass (shallow) whole genome sequencing. The DNA sequencing was performed on pre-capture genomic libraries, with an intended mean coverage of at least 0.1X, FASTQ files were cleaned by fastp and mapped to the reference human genome (GRCh38) with bwa.

  Dataset EGAD50000001497

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of three hyperdiploid ALL patients (ALLT-329, ALLT-347, ALLT-356). Sequencing libraries were made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using Illumina HiSeq X.

  Dataset EGAD50000002425

• Small‑scale mutations are infrequent as mechanisms of resistance in post‑PARP inhibitor tumour samples in high grade serous ovarian cancer

  Targeted DNA sequencing of high-grade serous ovarian cancer (HGSC) tumour and normal samples from 26 patients. Following target hybrid capture of 63 genes involved in DNA repair and response to treatment with an Agilent SureSelect XT panel, sequencing libraries were generated using the SureSelect XT Low Input Target Enrichment System (Agilent) as per the manufacturer's protocol. Libraries were sequenced on an Illumina NextSeq 500 at the Peter MacCallum Cancer Centre (Melbourne, Australia).

  Study EGAS50000000146

• L1 Retrotransposon sequencing in Cocaine Use Disorder - Study 1

  Cocaine Use Disorder (CUD) is a global public health problem, with no effective pharmacotherapies. While CUD is marked by high heritability, discovery of variants associated with risk for CUD has proven difficult. We used Restriction Enzyme Based Enriched L1 sequencing (REBELseq) to amplify L1 retrotransposons in gDNA isolated from medial prefrontal cortex NeuN+ neuronal nuclei from 25 CUD cases and 26 controls. Amplified libraries were sequenced on the Illumina HiSeq 4000 platform, and sequencing data was analyzed with the REBELseq bioinformatics pipeline.

  Study phs001966

• Chromatin accessibility in human monocyte differentiation

  This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting TET2, IRF4 and EGR2. In total, it includes 26 samples.

  Dataset EGAD00001006601

• Data files for PCGP SJACT RNASEQ

  This dataset contains RNA-Seq files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing.

  Dataset EGAD00001002680

• ICGC PCAWG Dataset: ORCA-IN_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ORCA-IN.

  Dataset EGAD00001002120