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• Exome sequencing of an AML treated with BCL2i

  Molecular profiling by exome sequencing of an AML case following treatment with a BCL2 inhibitor

  Dataset EGAD00001007307

• Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas: RNAseq variants

  Variants called from RNA-seq data of meningioma tumors.

  Dataset EGAD00001002649

• Ultraviolet radiation drives mutations in a subset of mucosal melanomas

  This dataset contains 20 whole genome sequences from 10 tumor-normal pairs from conjunctival melanomas.

  Dataset EGAD00001006568

• Reference epigenome IPS01_N_Fibroblast_smRNA-Seq data generated from KEP study

  A IPS01_N_Fibroblast_smRNA-Seq single end data for iPSC(Oct4)

  Dataset EGAD00001003501

• Reference epigenome CKD25_C_Podo_WGBS data generated from KEP study

  A CKD25_C_Podo_WGBS paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003470

• Reference epigenome CKD24_C_Podo_WGBS data generated from KEP study

  A CKD24_C_Podo_WGBS paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003469

• Reference epigenome IPS04_X_Fibroblast_mRNA-Seq data generated from KEP study

  A IPS04_X_Fibroblast_mRNA-Seq paired end data for iPSC(Oct4)

  Dataset EGAD00001003491

• Reference epigenome OB57_D_PreA_WGBS data generated from KEP study

  A OB57_D_PreA_WGBS paired end data for Preadipocyte(fat)

  Dataset EGAD00001003480

• Reference epigenome IPS01_N_Fibroblast_mRNA-Seq data generated from KEP study

  A IPS01_N_Fibroblast_mRNA-Seq paired end data for iPSC(Oct4)

  Dataset EGAD00001003488

• Reference epigenome IPS04_X_Fibroblast_smRNA-Seq data generated from KEP study

  A IPS04_X_Fibroblast_smRNA-Seq single end data for iPSC(Oct4)

  Dataset EGAD00001003504

• Transdisciplinary Research Into Cancer of the Lung (TRICL) - Exome Plus Targeted Sequencing

  The study was conducted under the auspices of the Transdisciplinary Research In Cancer of the Lung (TRICL) Research Team, which is a part of the Genetic Associations and MEchanisms in ONcology (GAME-ON) consortium, and associated with the International Lung Cancer Consortium (ILCCO). Ethics All participants provided written informed consent. All studies were reviewed and approved by institutional ethics review committees at the involved institutions. Sequencing data are derived from four sub-studies. The sub-studies that contributed include Harvard, Liverpool, Toronto, and IARC. The IARC and Toronto studies are described above. A description of the Harvard and Liverpool studies is provided below. Liverpool Lung Project: The Liverpool Lung Project (LLP)1 is a case control and cohort study, which has over 11,500 individuals, with detailed epidemiological, clinical and outcome data with associated specimens (i.e. tumour tissue, blood, plasma, sputum, bronchial lavage, EBUS and oral brushings). The participants have completed a detailed lifestyle questionnaire and updated data on clinical outcome and hospital events are collected through the Office of National Statistics, Cancer Registry and from Health Episode Statistics. The project is registered on the UK National Institute for Health Research (NIHR) lung cancer portfolio and has all the required ethical approvals and sponsorship arrangements in place. The LLP has detailed standard operating procedures (SOP) for all aspects of the recruitment, data, specimen collection as well as the data storage. The LLP Cohort study has 8,224 participants with blood and 7,761 with plasma samples. The LLP case-control samples have been incorporated into in a large number of international GWAS and molecular studies 2,3, methylation 4-7, microRNA 8and next generation studies 9-11, resulting in high ranking publications, as well as forming the basis for the LLP risk prediction model 12-14 which has been utilised in the UK lung cancer screening trial (UKLS) 15-17 Patient and control DNAs were derived from EDTA-venous blood samples. Harvard Samples. David Christiani at the Harvard University School of Public Health has been directing research studies to investigate etiological factors influencing lung cancer development since 1983 and has amassed a collection of 2000 controls and 5055 lung cancer cases. He has been actively collecting and storing snap frozen tumor samples since 1992. Around 1500 tumor samples have been collected and the average wet tumor yield is about 30 grams of tumor, of which 631 cases have completely annotated clinical and survival information. Pathology confirmation is provided by two pathologists. At the time of surgery, a minimum of 30 grams of wet lung tumor tissue and 30 grams of non-involved tissue from the same lobe is sectioned, flash frozen and sent to Dr. Christiani's lab for logging and storage. A blood sample for DNA and serum is collected. A structured interview by trained research staff is conducted on each case, and clinical outcomes and treatments is extracted and entered into the molecular epidemiology data base at Harvard. Fresh frozen samples have been collected from 1451 lung cancer and are available for study. Samples from this collaborative study have played key roles in major studies, including the initial finding describing EGFR mutations in lung cancer 22. Participants in this study are patients, > 18 years of age, with newly diagnosed histologically confirmed lung cancer. Samples that are included in the analysis have the following histologies: Adenocarcinoma: 8140/3, 8250/3, 8260/3, 8310/3, 8480/3 8560/3; LCC: 8012/3, 8031/3; squamous carcinoma: 8070/3, 8071/3, 8072/3, 8074/3; and other NSCLC: 8010/3, 8020/3, 8021/3, 8032/3, 8230/3. The Toronto Study: The Toronto study was conducted in the Great Toronto Area between 1997 and 2014. Cases were recruited at the hospitals in the network of University of Toronto and Lunenfeld- Tanenbaum Research Institute. At the time of recruitment in the clinical setting, provisional diagnoses of lung carcinoma were first assigned based on clinical criteria. Diagnoses for all cases included were histologically confirmed by the reference pathologist who is a specialist in pulmonary pathology, based on review of pathology reports from surgery, biopsy or cytology samples in 100% of cases. Diagnostic classification was done initially according to ICD-9, ICD-10, and ICD for oncology-2, and subsequently converted to ICD-O-3. Tumors were grouped into the major categories included in this analysis according to primary cancer type based on the ICD-3 definitions. Controls were randomly selected from individual visiting family medicine clinics and Ministry of Finance Municipal Tax Tapes. All subjects were interviewed using a standard questionnaire and information on lifestyle risk factors, occupational history, medical and family history was collected. Blood samples were collected from more than 85% of the subjects. IARC: The IARC data are derived from case-control studies conducted in Russia and include samples that have available tissue samples. Patient and control DNAs were derived from EDTA-venous blood samples. The lung cancer patients were classified according to ICD-O-3; SQ: 8070/3, 8071/3, 8072/3, 8074/3; AD: 8140/3, 8250/3, 8260/3, 8310/3, 8480/3, 8560/3, 8251/3, 8490/3, 8570/3, 8574/3; with tumous with overlapping histologies classified as mixed. The Lung Cancer Transdisciplinary Research Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" section of this top-level study page phs000876 Lung Cancer Transdisciplinary Research Cohort. phs000877 Meta Analysis phs000878 CIDR Lung Cancer phs001681 Affy Axiom Array

  Study phs000876

• Immunoreactive_p53_areas_in_human_skin_2

  Previous work has suggested that in mice there may be a difference in mutational burden between areas expressing stabilised p53 protein and others. We wish to see if this observation holds true in human sun-exposed epidermis. We will take 0.25mm punch biopsies from peeled human skin epidermis which will be submitted to the low input pipeline prior to sequencing.

  Study EGAS00001004463

• Copy number analysis of Diamond-Blackfan Anemia (DBA) using SNP array

  Diamond–Blackfan anemia (DBA), is a rare congenital anemia that usually presents in infancy. About fifty percent of DBA patients possess mutations in ribosomal protains (RPs). In this study, we performed genomic copy number analysis using SNP arrays for 27 Japanese DBA patients to detect genomic copy number lesions of the RP genes' loci.

  Study EGAS00000000105

• Genomic Sequencing of Solitary Fibrous Tumors

  Solitary fibrous tumors (SFTs) are rare mesenchymal tumors that can be benign or malignant. In this study, we sequenced and analyzed the exomes of 17 SFT matched tumor and normal pairs. This study appertains to a large endeavor to characterize cancers as part of the Slim Initiative for Genomic Medicine in the Americas (SIGMA) project.

  Study phs000568

• TREM2+ Cells in Human Basal Cell Carcinomas

  To explore the tumor immune microenvironment heterogeneity in sporadic human basal cell carcinoma tumors, we profiled two individual patient tumors by scRNA-Seq. We identified a population of TREM2+ macrophages, which have been implicated in promoting an immunosuppressive tumor microenvironment. We identify that TREM2+ can promote tumor epithelial proliferation in an immunosuppressive independent manner.

  Study phs003242

• NHLBI TOPMed: The Vanderbilt Atrial Fibrillation Registry (VU_AF)

  The Vanderbilt Atrial Fibrillation (AF) Registry was founded in 2001. Patients with AF and family members are prospectively enrolled. At enrollment a detailed past medical history is obtained along with an AF symptom severity assessment. Blood samples are obtained for DNA extraction. Patients are followed longitudinally along with serial collection of AF symptom severity assessments.

  Study phs001032

• Genome Wide Association Studies in ECOG 2997 Trial

  The ECOG 2997 trial was a randomized controlled trial for patients with previously untreated CLL comparing fludarabine monotherapy to the combination of fludarabine and cyclophosphamide. The initial clinical findings of this study were published in the Journal of Clinical Oncology in 2007 (JCO 25:793-8). Additional laboratory studies have also published (JCO 25:799-804).

  Study phs000621

• The Genetic Landscape of Mutations in Burkitt Lymphoma

  Burkitt lymphoma (BL) is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. We sequenced exomes of 59 BL tumors, 14 of which had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a novel tumor suppressor gene.

  Study phs000562

• Determinants of Asthma Following RSV Bronchiolitis in Early Life

  The goal of the RSV Bronchiolitis in Early Life (RBEL) study is to determine how specific genetic, biologic, and immunologic characteristics interact to predispose individuals to develop asthma. Participants were carefully recruited by selecting a prospective cohort of 206 infants with severe respiratory syncytial virus (RSV) bronchiolitis who were at substantial risk of developing asthma.

  Study phs001009

• Spatiotemporal Analysis of the Human Cerebellum

  We sought to characterize neural progenitors within spatially demarcated regions of the human cerebellum at a molecular level during neurogenesis. We used laser-capture microdissection to enrich for cells within the ventricular zone and subventricular zone regions of the rhombic lip, external granule cell layer and Purkinje cell layer, then performed RNA-sequencing on the enriched samples.

  Study phs001908

• RareBliss: Rare Bipolar Loci Identification Through Sequencing Study

  Bipolar disorder is a complex psychiatric disease for which few causative genes have been discovered. Targeted sequencing of bipolar cases and unaffected controls was performed to elucidate the contribution of rare variants to bipolar disorder. This study included the standard exome targets as well as genes involved in synaptic function and genes previously implicated in bipolar disorder.

  Study phs001358

• Vulnerabilities of Midbrain Dopaminergic Neurons to Parkinson's Disease Revealed by Single-Cell Genomics

  We developed a novel protocol for the enrichment of midbrain DA neurons from frozen tissue. We subsequently performed single-nuclei RNA-sequencing on enriched samples from postmortem midbrain tissue from human, macaque, tree shrew, rat, and mouse. We identified vulnerable and resistant populations from these data and associated genetic enrichments and differential expression changes.

  Study phs002879

• Myelodysplastic Syndrome (MDS) in Humanized Mice

  This study was to develop a faithful pre-clinical MDS patient-derived xenotransplantation model in cytokine-humanized immunodeficient "MISTRG" mice. We performed targeted genome sequencing on bone marrow from patients with MDS or AML and from bone marrow of mice engrafted with the respective patient bone marrow. Cytokine-humanized immunodeficient mice faithfully replicate human MDS.

  Study phs001778

• Autosomal Recessive CD55 Deficiency is Associated with Protein Losing Enteropathy, Thrombosis, and Complement Dysregulation

  We describe 11 patients from 8 families with homozygous LOF mutations in the complement regulatory protein CD55. Loss of CD55 is associated with increased complement activation, severe protein losing enteropathy accompanying a primary intestinal lymphangiectasia, and deep vein thrombotic events. We have named this disease CHAPLE after the principle components of the disease.

  Study phs001376

• Whole Exome Sequencing of Six Signet Ring/Plasmacytoid Variant Bladder Tumors

  In this study, six plasmacytoid bladder cancers were analyzed by whole exome sequencing. The results show loss of the CDH1 gene in every sample and correlate with E-cadherin loss of expression by immunohistochemistry. A separate validation cohort of plasmacytoid samples showed loss of E-cadherin expression by CDH1 mutation or promoter hypermethylation.

  Study phs001064

• Rapid Acceleration of Diagnostics - Digital Health Technologies' (RADx-DHT) Collection of General Research Use Datasets

  This individual-level collection of datasets contains all the RADx Digital Health Technologies (RADx-DHT) studies in dbGaP for General Research Use (GRU). Access to studies in this collection is on the RAPIDS platform. To request access to this study collection, select phs003666 in the dbGaP when submitting a data access request.

  Study phs003666

• Multiregion exome sequencing of ovarian immature teratomas

  Tumor tissue from each of the indicated ovarian and disseminated GCT components was selectively punched from formalin-fixed, paraffin-embedded blocks. Genomic DNA was extracted from these tumor and matched normal tissue samples, with a total of 500 ng of genomic DNA used as input for capture employing the xGen Exome Research Panel.

  Study EGAS50000000291

• Enhanced resolution profiling in twins reveals differential methylation signatures of Type 2 Diabetes with links to its complications

  We profiled DNA methylation in blood samples from participants of European ancestry from 7 twin cohorts using a methylation sequencing platform targeting regulatory genomic regions encompassing 2,048,698 CpG sites. The results help to improve our understanding of T2D disease pathogenesis and progression and may provide biomarkers for its complications.

  Study EGAS50000000197

• Single cell transcriptomic profiles of advanced melanoma patients treated with checkpoint inhibitor immunotherapy

  Little is known about the resistant clones within the tumour ecosystem treated with immunotherapy. This work provides a comprehensive and integrative analysis of each individual non-responding melanoma patients, including clinical features integrated with single cell analysis, which is critical to understand features of resistance in order to improve cancer patients’ outcomes.

  Study EGAS50000000339

• DCLRE1B/Apollo germline mutations associated with renal cell carcinoma

  Highlights of Bories et al. article submitted to BBA - Molecular Basis of Disease: We identified 2 germline mutations in the DCLRE1B gene encoding the Apollo protein by Whole Exome Sequencing (WES) in two families with inherited clear-cell Renal Cell Carcinoma. Our study suggests a putative link between DNA repair, telomere protection and renal oncogenesis.

  Study EGAS50000000216

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids, aimed at measuring the spontaneous rates of accumulation of new single-nucleotide sequence variations in seven microsatellite stable CRCs and one microsatellite unstable CRC. Mutations accumulated over six+six months were identified via whole genome sequencing of clonal tumoroids. 150x WGS for 7 samples.

  Study EGAS50000000425

• PDX gene expression

  Investigation of the anti-tumor activity of the potent, highly selective, orally bioavailable CHK1 inhibitor (CHK1i), SRA737, in both acquired PARPi-resistant BRCA1/2 mutant and CCNE1amp high-grade serous ovarian cancer (HGSOC) models. We analyzed gene expression in five patient derived xenografts (PDX) that responded to CHK1i and three PDX that had a poor response to CHK1i.

  Study EGAS50000000084

• Tumor Normal Pair for SV mosaic

  Simulated (based on real world data) tumor normal pair designed for benchmarking and optimisation of structural variation callers. The calls are derived from 12 patients in the hartwig database requested by the EUCANCan project. Paired-end sequencing data was imputed into the normal reference data to simulate real world variation like purity as well as technical impact of sequencing technologies. The dataset contains a tumor sequenced to ±90x depth and a normal control sequenced to ±30 x depth of these imputed events. The break junctions of all detected SVs in the original cases are imputed in this data from diagnostic WGS sequencing data.

  Dataset EGAD50000000668

• sWGS data from 362 tumor with non muscle invasive bladder cancer and 30 blood samples (15 males and 15 females)

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 876 BAM files corresponding to the full WES dataset. This dataset contains 392 BAM files corresponding to the full sWGS dataset. Tumor samples were sequenced to median coverage of 2.14x (1.24-9.01).

  Dataset EGAD50000000732

• Single cell whole genome sequencing of luminal breast epithelial cells from wildtype and BRCA mutation carriers

  Single cell whole genome sequencing was done using DLP+ (https://doi.org/10.1016/j.cell.2019.10.026) on luminal breast epithelial cells from wildtype and BRCA mutation carriers. Each BAM file is a merged BAM from single cells from a single sample, and the cells can be uniquely identified by their @RG group. Only high quality cells were kept, thus there are large differences in BAM sizes. The same sample/patient can be found across multiple BAM files to accumulate more cells, sometimes the same patient will have multiple FACS sorted cell types also split by BAMs.

  Dataset EGAD50000000883

• scRNA-seq dataset, RCC

  scRNA-seq dataset for the study "Surgery in combination with immune checkpoint therapy as an effective treatment for patients with metastatic cancer." The dataset comprises 38 samples from 19 patients, with each pair includes a baseline (BL) sample and a post-biopsy or post-surgery sample. Each sample corresponds to an R1 (read 1) and an R2 (read 2) files (.fastq.gz) for paired reads. Beside procedure (biopsy or surgery), another important phenotype is response (PR and PD in this case, no SD for these patients), included in the description of the samples. The sequencing was performed using Illumina NovaSeq 6000 platform., as seen in the experiment description.

  Dataset EGAD50000000566

• Glucose Binds and Activates NSUN2 to Promote Translation and Epidermal Differentiation

  This study was undertaken to determine the role of NSUN2 in epidermal homeostasis. Primary neonatal foreskin keratinocytes were obtained from discarded surgical samples at a California hospital. Samples were anonymous and not selected. NSUN2 was found to promote epidermal differentiation and alter translation using the methods of RNA-seq, CLIP-seq and Ribo-seq.

  Study phs003767

• iNHL WXS Data Commitee

  The iNHL WXS Data Commitee is responsible for managing access to datasets submitted to the European Genome-phenome Archive (EGA). Our committee ensures that access requests are evaluated in compliance with ethical guidelines, regulatory requirements, and the conditions specified by data submitters. Researchers requesting access to these datasets must provide a clear and valid scientific purpose, demonstrate affiliation with a recognized institution, and agree to the terms of use outlined in the Data Access Agreement. The iNHL WXS Data Commitee works to uphold data privacy and security while facilitating responsible data sharing to advance scientific discovery. For further information on our policies or the application process, please contact Hauke Busch (hauke.busch@uni-luebeck.de).

  Dac EGAC50000000488

• Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  PPM1D, a central regulator of the DNA damage response, is commonly mutated in therapy-related clonal hematopoiesis (CH), acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). PPM1D mutations have been shown to expand under selective pressure of DNA-damaging chemotherapy. However, whether PPM1D mutations promote the development of hematologic malignancies remains unclear.

  Study EGAS50000000840

• Alpha synucleinopathy spectrum - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA seq dataset from prefrontal cortex for a total of N=44 samples. Tissue samples correspond to patients with different alpha synucleinopathies. Specifically, idiopathic Parkinson's disease (PD, N=20) monogenic PD caused by LRRK2 mutations (LRRK2-PD, N=7), multiple system atrophy (MSA, N=6) and neurologically healthy controls (N=11). RNA seq was carried out using ribosomal depletion. The totality of these samples were also sequenced using single nucleus RNA seq, and available within the same study as a separate dataset.

  Dataset EGAD50000000430

• Alpha synucleinopathy spectrum - single nucleus RNA seq of prefrontal cortex

  Single nucleus RNA seq dataset from prefrontal cortex of a total of N=46 individuals with alpha synucleinopathies and healthy controls. Tissue samples correspond to patients with Parkinson's disease (PD, N=20) monogenic PD caused by LRRK2 mutations (LRRK2-PD, N=7), multiple system atrophy (MSA, N=6) and neurologically healthy controls (N=13). RNA seq was carried out employing 10X Genomics Chromium. These samples were also sequenced using conventional bulk tissue RNA seq, and available within the same study as a separate dataset.

  Dataset EGAD50000000431

• SUM-seq data for spontaneous differentiation of iPSCs upon perturbation of GATA2, NR4A2 or SOX17

  We combined SUM-seq with arrayed CRISPR screening, modulating the expression of key lineage transcription factors (TFs) (GATA2 - mesoderm, SOX17 - endoderm, and NR4A2 - neuroectoderm) in hiPSCs via CRISPR interference (CRISPRi) or activation (CRISPRa) over a time course of spontaneous differentiation (days cultured in vitro: 0, 4, 12, and 18). This totalled to 54 samples (4 day/time points x 3 target TFs x 2-3 gRNAs per target x CRISPRi/a). Single-cell chromatin accessibility and gene expression data is provided as demultiplexed fastq files.

  Dataset EGAD50000001205

• Variables of diversity, clonality, V and J usage and main COVID-19-reactive GLIPH2 frequencies.

  Main results of the T cell repertorie analysis of a cohort of 61 patients. For each patient, repertorie diversity and clonality metrics, V an J alelle frequency and COVID-19-reactive sequencies have been calculated using open.source code. For more information about the study, please visit DOI: 10.1186/s40246-024-00654-0

  Study EGAS50000000587

• An epidemiological study examining the relationship among food, health, and genome

  We conducted a cohort-based study to investigate the association between the genetic background and diet/lifestyle in 962 healthy Japanese. We analyzed the Ebetsu cohort and some participants living in Tokyo. The SNP array (Japonica Array v2) was used for genotyping. Shotgun metagenomic sequencing of fecal microbiome and metabolome of feces and blood were analyzed.

  Study JGAS000678

• Merged VCF file from familial Meniere disease cohort

  This dataset contains a merge VCF file generated from WES data of patients diagnosed with familial Meniere disease (FMD). Variant calling followed GATK best practices using the nf-core/Sarek pipeline (v3), and variants were filtered using genotype-level thresholds consistent with gnomAD filters. Multiallelic variants were split and INDELs were left-aligned during normalization. Variant Quality Score Recalibration (VQSR) was applied separately to SNVs and INDELs using well-established truth sets, with a 90% sensitivity threshold to maximize the detection of rare variants. Final variants were annotated with Ensembl VEP.

  Dataset EGAD50000001682

• Merged VCF file from sporadic Meniere disease cohort

  This dataset contains a merge VCF file generated from WES data of patients diagnosed with sporadic Meniere disease (FMD). Variant calling followed GATK best practices using the nf-core/Sarek pipeline (v3), and variants were filtered using genotype-level thresholds consistent with gnomAD filters. Multiallelic variants were split and INDELs were left-aligned during normalization. Variant Quality Score Recalibration (VQSR) was applied separately to SNVs and INDELs using well-established truth sets, with a 90% sensitivity threshold to maximize the detection of rare variants. Final variants were annotated with Ensembl VEP.

  Dataset EGAD50000001683

• Amplicon based re-sequencing of multi-region PDAC samples

  Multi-region tumor samples were cut from frozen sections or FFPEs and reviewed from microdissection and H&E staining in order to select ones with high cellularity. DNA extraction was done using DNeasy Blood & Tissue Kits for frozen samples following the manufacturer’s guideline. Extracted DNAs were processed on an Illumina HiSeq 2500 in a paired end mode (100x100) using a custom targeted panel based on the list of all unique somatic mutations from the original WES data by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center (New York, NY).

  Dataset EGAD50000000354

• Paraganglioma Smart-Seq2 Single Nuclei Sequencing Data

  Paraganglioma is a rare neuroendocrine tumor that originates from chromaffin cells of the adrenal medulla or extra-adrenal paraganglia. This study aims to investigate the heterogeneity of this tumor and to identify potential biomarkers associated with its malignancy. To achieve this, we performed single-nucleus RNA sequencing of human paraganglioma samples using the SMART-Seq2 protocol.

  Study EGAS50000001184

• Single-cell RNA sequencing of metastatic colorectal cancer organoids treated with cetuximab

  Single-cell RNA sequencing was performed on metastatic colorectal cancer (mCRC) organoids derived from a cetuximab-sensitive patient-derived xenograft (PDX) model. The objective of this analysis was to investigate, at single-cell resolution, the transcriptional changes previously identified in bulk RNA-seq analyses of PDX models exposed to anti-EGFR therapeutic pressure.

  Study EGAS50000001460

• HNF1B induced three-dimentional genome analysis of patient-derived pancreas neoplasm organoids

  Three-dimensional (3D) genome structures are organized in a hierarchy of various module layers, including chromosome compartment, topologically associating domain, and enhancer-promoter loop. These modules are important in regulating cell type specific gene expression. Here, we aimed to elucidate how 3D genome organization is related to regulating subtype specific genes in pancreatic neoplasms.

  Study JGAS000514