14666 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Investigating the genetics of immunity against Salmonella in humans (2019-09-05)

  This study entails whole genome sequencing of an interleukin (IL)-12 b-1 receptor-deficient individual who presented with a chronic systemic Salmonella Enteritidis infection that did not resolve with standard IFNg and antibiotic treatment. Whole genome sequencing of the patient's parents are also included. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-09-05.

  Dataset EGAD00001005311

• Exome Sequencing to Identify Causes of Leukaemia Predisposing Congenital Neutropenias (2019-08-19)

  The objective of this study is to identify the causative genes in two unrelated congenital neutropenia families. We aim to whole exome sequence the affected individuals, unaffected siblings and parents in both cases in an effort to idenitfy the causative genetic mutation. Exome capture will be performed using Agilent SureSelect system. Subsequently, exome libraries will sequenced using the Illumina HiSeq platform. Sequence variant calling will be done in house and common variants excluded using public databases and data from unaffected family members. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005264

• RNA and ChIP Sequencing datasets from the study Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma

  This dataset contains the RNA and ChIP Sequencing data from the study Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma. The data is organized in 7 experiments which are divided by both sequencing technology or the application of siRNA or drug interventions (or lack thereof) on neuroblastoma cell lines. The experiment names and the file names have been chosen in each respective experiment to guide future users of the data to replicate the analyses in the manuscript.

  Dataset EGAD00001006964

• Single-cell RNA-seq data from metastatic ovarian cancer for quality control study

  Quality control is a crucial preliminary step in any single-cell RNAseq experiment, where hard thresholds are commonly used. In order to develop a methodology for a more precise cell filtering in the early steps of a scRNAseq data analysis, we collected tissue samples before chemotherapy from 4 patients.

  Study EGAS00001005066

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (Exome)

  Sequencing of LCM-derived microbiopsies from 10 women who underwent reduction mammoplasty. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who are BRCA1/2 germline carriers and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010110

• MutWP5: CRUK Mutographs of Cancer: BRCA Carriers (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastecomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010112

• Single-cell RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015710

• Single-cell RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015717

• Single-cell ATAC-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell ATAC sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015719

• Single-cell ATAC-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell ATAC sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015711

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 10 women who underwent reduction mammoplasty. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who are BRCA1/2 germline carriers and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010113

• Single-cell ATAC-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell ATAC sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015715

• MutWP5: CRUK Mutographs of Cancer: BRCA Carriers (Exome)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastecomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010115

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (Exome)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 10 women who underwent reduction mammoplasty. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who are BRCA1/2 germline carriers and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010116

• Comprehensive copy number aberration analysis using digital Multiplex Ligation-dependent Probe Amplification (digitalMLPA) in pediatric B-cell precursor acute lymphoblastic leukemia

  In this study a next-generation sequencing based method was applied to comprehensively screen for recurrent, disease-relevant copy number aberrations in a cohort of Hungarian patients. Diagnostic bone marrow samples from 260 children with B-cell acute lymphoblastic leukemia as well as 72 control samples and were investigated by digital multiplex ligation-dependent probe amplification using the disease-specific D007 probemix. Whole chromosome gains and losses, as well as subchromosomal copy number aberrations were simultaneously profiled.

  Dataset EGAD00001010878

• NIH Division of Intramural Research Multiomic Monogenic Disease Study

  This cross-sectional, observational study utilized high-dimensional approaches, including transcriptomic analysis, serum protein profiling, and peripheral blood frequency assessments, to compare 228 adult and pediatric patients diagnosed with 22 monogenic immune-mediated conditions impacting various key immunological pathways, with 42 age- and sex-matched healthy controls. Participants were enrolled in clinical protocols at the National Institutes of Health in Bethesda, Maryland, USA. The primary objectives of the study were twofold: first, to identify disease-specific and shared "pan-disease" signatures using the collected data, and second, to develop a Random Forest classifier integrating these datasets to differentiate between age- and sex-matched healthy individuals and monogenic patients. This classifier produced a metric known as the "Immune Health Metric" (IHM). Subsequent analysis demonstrated that the IHM effectively distinguished healthy subjects from individuals with multiple polygenic autoimmune and inflammatory diseases in independent datasets. Moreover, it exhibited correlations with healthy aging and tracked disease activities and treatment responses across both immunological and non-immunological conditions. Additionally, the IHM accurately predicted age-dependent antibody responses to various vaccines, including influenza, Hepatitis A/B, Yellow Fever, Varicella Zoster, and Meningococcal vaccines.The microarray-based transcriptomic data, aptamer-based serum protein concentrations (Somalogic platform), peripheral blood frequency data, and clinical information will be made accessible through the database of Genotypes and Phenotypes (dbGaP).

  Study phs002732

• A Perioperative Study of Safusidenib in Patients with IDH1-Mutated Glioma

  10 participants with a radiological or pathological diagnosis of WHO Grade 2 lower-grade glioma (LGG) were recruited at a single center starting in December, 2022. Eligibility criteria permitted participants who had undergone prior surgery for WHO Grade 2 LGG, but excluded those with a history of prior radiation or chemotherapy.In Part A of the study, participants underwent an initial craniotomy with tumor biopsy and a lumbar puncture for cerebrospinal fluid (CSF) collection at study entry. Following sample collection, participants received safusidenib at the recommended phase 2 doses of 250 mg twice daily (b.i.d.) for a period of 22–36 days. This was followed by a second craniotomy for maximal safe tumor resection and a repeat lumbar puncture within 5 hours of the final pre-resection dose of safusidenib. Tumor, blood, and CSF samples were collected at both surgical time points for comprehensive translational research.Molecular analyses were performed on samples collected at both time points. These included pharmacokinetics (PK), targeted metabolomics, whole-genome sequencing (WGS) of tumor tissue, single-nucleus RNA sequencing (snRNA-seq), and DNA methylation profiling on all patients. Targeted metabolomics was conducted on samples from 9 participants, while spatial transcriptomics and spatial metabolomics were performed on tumor tissue from 3 participants each. Histone methylation profiling was conducted on samples from 8 participants.

  Study phs003976

• Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Coronary Artery Risk Development in Young Adults Study (CARDIA)

  Cohort Description The Coronary Artery Risk Development in Young Adults (CARDIA) study is a study examining the development and determinants of clinical and subclinical cardiovascular disease and their risk factors. It began in 1985-6 with a group of 5115 black and white men and women aged 18-30 years. The participants were selected so that there would be approximately the same number of people in subgroups of race, gender, education (high school or less and more than high school), and age (18-24 and 25-30 years) in each of 4 centers: Birmingham, AL; Chicago, IL; Minneapolis, MN; and Oakland, CA. These same participants were asked to participate in follow-up examinations during 1987-1988 (Year 2), 1990-1991 (Year 5), 1992-1993 (Year 7), 1995-1996 (Year 10), 2000-2001 (Year 15), 2005-2006 (Year 20), 2010-2011 (Year 25), 2015-2016 (Year 30), and 2021-2022 (Year 35). Data Being Submitted Wave 1 questionnaire data includes 397 variables for up to 2434 CARDIA participants in C4RWave 2 questionnaire data includes 448 variables for up to 1901 CARDIA participants in C4RDried Blood Spot/Serosurvey data includes 7 variables for up to 1332 CARDIA participants in C4RDerived data includes 43 variables for up to 2723 CARDIA participants in C4RPhenotype data includes 113 variables for up to 2723 CARDIA participants in C4R

  Study phs003045

• Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment

  Study EGAS00001003886

• Oncoscan CNV FFPE SNP-arrays (Affymetrix, Thermo Fisher Scientific) for the study "Molecular profiling of EBV associated diffuse large B-cell lymphoma"

  Dataset EGAD00010002363

• International Parkinson's Disease Genomics Consortium (IPDGC), NeuroX Dataset

  Expanded replication set based on Nalls et al. 2014.

  Study phs000918

• Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single nucleotide variants and tumoral heterogeneity by massively parallel sequencing

  Study EGAS00001000370

• Preeclampsia InterPregGen Consortium: GWAS meta-analysis summary statistics for European fetal preeclampsia cases versus controls and GWAS genotype data for European fetal preeclampsia cases

  Study EGAS00001001048

• LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients

  Study EGAS00001007072

• Single-cell RNA-seq of murine splenocytes from Bcl6tg/+ and Cd70-/-; Bcl6tg/+ diffuse large B-cell lymphoma mouse models and Cd70-/- and wild-type controls.

  Study EGAS00001007570

• Methylation data

  To ellucidate methylation activity in mRCC, methylation data was generated as part of the EuroTarget study

  Dataset EGAD50000002295

• BAP1_sequence_of_uveal_melanoma_cell_lines

  Detection of BAP1 mutations in DNA from 3 uveal melanoma cell lines.

  Study EGAS00001001520

• Pseudogene_RNAseq

  RNA sequencing to validate findings of somatic pseudogenes acquired during cancer development

  Study EGAS00001000606

• Low_input_LC__ISC_

  R&D project to develop low input library construction methods.

  Study EGAS00001001856

• Chugai_colorectal_organoid_sequencing

  Genomic and transcriptomic characterization of drug-resistant colon cancer stem cell lines.

  Study EGAS00001000872

• Reference epigenome IPS06_X_ENeuron_WGBS data generated from KEP study

  A IPS06_X_ENeuron_WGBS paired end data for Early neuron cells(Tuj1)

  Dataset EGAD00001003478

• Carcinoid study - WES dataset

  Fernandez-Cuesta et al, 2014, Nature Communication, Whole exome sequencing data set

  Dataset EGAD00001000820

• Reference epigenome OB56_N_PreA_mRNA-Seq data generated from KEP study

  A OB56_N_PreA_mRNA-Seq paired end data for Preadipocytes(fat)

  Dataset EGAD00001003486

• Reference epigenome ADMSC07 h3k4me1 ChIP-Seq data generated from KEP study

  ADMSC07 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007391

• MPNST exome and genome

  This is the complete dataset (exome and genome) for the EGAS00001000974 study.

  Dataset EGAD00001001040

• CONTAGIOUS trial - COVID-19 16S metadata

  Study metadata, containing the clinical information on samples and patients

  Dataset EGAD00001008006

• Reference epigenome IPS05_X_NPC_WGBS data generated from KEP study

  A IPS05_X_NPC_WGBS paired end data for Neural progenitor cells(Nestin)

  Dataset EGAD00001003477

• Methylome profiling of epithelioid sarcoma

  Explore the methylome landscape of epithelioid sarcoma using array data.

  Study EGAS00001007257

• Somatic_mutation_in_edited_cholangiocyte_organoids_WGS

  Characterisation of mutation rates and patterns in edited human cholangiocyte organoids (WGS)

  Study EGAS00001006326

• Genomic analyses to identify metabolic vulnerabilities

  Genomic analyses to identify metabolic vulnerabilities on PDX samples

  Study EGAS00001007244

• Gene expression from human iPSC derived motor neurons.

  Gene expression from human iPSC derived motor neurons.

  Study EGAS00001003785

• Transcriptomic profiling of lymphedema

  RNA-seq of skin from human subjects with and without lymphedema

  Study EGAS00001004516

• Psoriatic_arthritis_WGS

  Whole genome sequencing of immune cells from patients diagnosed with psoriatic arthritis

  Study EGAS00001002822

• Infant_Spindle_Tumour_Study

  We aim to describe the transcriptomic landscape of infant spindle cell tumours.

  Study EGAS00001002935

• Plasma DNA profile in DNASE1L3 deficiency-Mouse AAV samples

  Plasma DNA profile in DNASE1L3 deficiency-Mouse AAV

  Study EGAS00001004409

• PBMC_dual_10X_kit

  Dual snRNAseq and ATACseq of replicate PBMC samples for 10X beta testing.

  Study EGAS00001004834

• Settlement of Polynesia

  Genotypes used to reconstruct the settlement timings and paths of Polynesia.

  Study EGAS00001005362

• HCA_Muscle_Adult_Wellcome_RNA_Managed_Access

  Transcriptomic analysis of skeletal muscle, to understand the mechanisms of muscle ageing.

  Study EGAS00001007495

• Cellular Diversity of the Developing Human Cerebral Cortex

  We sought to characterize cellular heterogeneity in the human cerebral cortex at a molecular level during cortical neurogenesis. We captured single cells and generated sequencing libraries using the C1TM Single-Cell Auto Prep System (Fluidigm), the SMARTer Ultra Low RNA Kit (Clontech), and the Nextera XT DNA Sample Preparation Kit (Illumina). We performed unbiased clustering of the single cells and further examined transcriptional variation among cell groups interpreted as radial glia. Within this population, the major sources of variation related to cell cycle progression and the stem cell niche from which radial glia were captured. We found that outer subventricular zone radial glia (oRG cells) preferentially express genes related to extracellular matrix formation, migration, and stemness, including TNC, PTPRZ1, FAM107A, HOPX, and LIFR and related this transcriptional state to the position, morphology, and cell behaviors previously used to classify the cell type. Our results suggest that oRG cells maintain the subventricular niche through local production of growth factors, potentiation of growth factor signals by extracellular matrix proteins, and activation of self-renewal pathways, thereby contributing to the developmental and evolutionary expansion of the human neocortex. For study version 2, we have updated this data set to include additional primary cells that we infer to represent microglia, endothelial cells, and immature astrocytes, as well as additional cells from the developing neural retina, and from iPS-cell derived cerebral organoids. The genes distinguishing these cell populations may reveal biological processes supporting the diverse functions of these cell types as well as vulnerabilities of specific cell types in human genetic diseases and in viral infections. For study version 3, we have updated the data set to include additional primary cells, including those published in Nowakowski et al., 2017 (PMID:29217575). For study version 4, we have additionally performed parallel analyses of transcriptomes and physiological responses of 476 single cells isolated from developing human cortex. As a result, we were able to identify physiological response profiles of specific progenitor and neuronal cell types during human cortical development.For study version 5, we have additionally performed bulk RNA sequencing of organotypic primary cultures from the developing human cortex with or without exposure to SARS-CoV-2 to understand the infectability and transcriptomic effects of SARS-CoV-2 on the developing human cortex.For study version 6, we investigated the impact of LIFR signaling on neural proliferation and differentiation of human oRG cells. Specifically, we isolated oRG cells from the primary developing neocortex and cultured them for four weeks with and without LIF treatment. We then performed single-cell RNA sequencing using the Chromium Single Cell 3’ Reagent Kits (v3.1, Dual index) from 10x Genomics to understand the molecular and cellular changes of oRG differentiation upon LIF treatment.

  Study phs000989

• Efficacy of a Therapeutic Treatment Trial in Angelman Syndrome

  This study has been designed to evaluate the possible therapeutic benefits of L-5-methyltetrahydrofolate (Metafolin), vitamin B12, creatine and betaine in children with Angelman Syndrome (AS). This study is based on the hypotheses 1) that dietary manipulation may increase global DNA methylation; 2) that increased methylation of the paternal chromosome in AS participants may increase expression of the Angelman gene causing clinical benefit; and 3) that dietary interventions with Metafolin in conjunction with creatine, betaine, and vitamin B12 would represent little risk, but some chance for benefit. The dietary regimen is felt to be quite benign and safe. The clinical response will be measured by recording: changes in seizure activity, changes in communication skills, changes in developmental skills and changes in behavioral patterns as indicated by formal developmental assessments and clinical evaluations. We will assess the progress of the participants by monitoring their changes from baseline throughout their participation in the study and measure their improvement in particular in the developmental parameters. As a secondary aim, we plan to measure the biochemical response to these compounds by obtaining levels of homocysteine, methionine, S-adenosyl-methionine (SAM), and S-adenosyl-homocysteine (SAH). The molecular response will be measured by global DNA methylation analysis. As an exploratory aim, we hope to use control data we have previously obtained from a double blind placebo-controlled trial done in the past using betaine and folic acid to compare the development of those children who have and those who have not received medications. More specifically, we wish to compare differences in the rate of development for those children who have never received study medications (from the first trial) with those who have received medications from the present trial. Developmental parameters used in the previous trial will be consistent with those used in the present trial in order to permit these comparisons. The previous trial was conducted at Baylor College of Medicine, Rady San Diego Children's Hospital and Boston Children's Hospital whereas a group of AS participants received folic acid and betaine or placebo in a randomized double-blind basis. All the participants for the study will include patients who have a documented molecular diagnosis of AS. The participants will be seen at Baylor College of Medicine, Rady Children's Hospital of San Diego, Boston Children's Hospital and the Greenwood Genetics Center at 0 months and at 12 months for follow-up. Clinical and relevant historical data will be collected during the clinical visit and examination and also by reviewing medical and laboratory records. This information will then be entered into a HIPAA compliant clinical research database.

  Study phs000701