Explore a diverse collection of biomedical datasets contributed by renowned research initiatives. Access genomics data, proteomics data, disease progression, and clinical studies across conditions like Alzheimer’s, Parkinson’s, cardiovascular disease, cancer, autoimmune disorders, and rare genetic disorders such as neurofibromatosis.
AMP RA/SLE Phase II CyTOF of PBMC samples profiling marker panels targeting T cells, B cells, myeloid cells, and NK cells and total leukocyte (TL) samples profiling a marker panel targeting granulocytes.
The MyHeart Counts Cardiovascular Health Study is a smartphone-based study of cardiovascular health, consisting of records of daily physical activity, health questionnaires, and 6-minute walk fitness tests.
This study provides post-mortem whole genome sequencing and brain bulk RNA sequencing data from over 850 individuals, including 288 Black or African American individuals and 330 Hispanic individuals representing the spectrum of Alzheimer’s Disease phenotypes.
mPower is a large, longitudinal study which piloted new approaches to monitoring key indicators of Parkinson disease progression and diagnosis incorporating traditional behavioral symptom measurements along with novel metrics gleaned from sensor-rich mobile devices.
Single-cell Gene Expression Data from the Breast Pre-Cancer Atlas
This includes single-cell gene expression at all levels, from raw data to processed data that can also be visualized in CELLxGENE. The dataset seeks to illuminate the role of specialized cells in in pre-cancer women with breast cancer risk factors.
Latest release of the data within GENIE BPC NSCLC shared with the global research community. The database currently contains CLIA-/ISO-certified genomic data obtained during the course of routine practice at multiple international institutions and expanded clinical data from de-identified patients treated at the institutions participating in AACR Project GENIE.
Latest release of the data within GENIE BPC CRC shared with the global research community. The database currently contains CLIA-/ISO-certified genomic data obtained during the course of routine practice at multiple international institutions and expanded clinical data from de-identified patients treated at the institutions participating in AACR Project GENIE.
AMP RA Phase II synovium 10x Genomics scATAC-seq data from RA and OA control cases. Twenty-four chromatin classes were identified which are proposed to represent ‘superstates’ corresponding to multiple transcriptional cell states as described in Nature Communications https://doi.org/10.1038/s41467-024-48620-7.
AMP RA Phase II synovium CITE-seq data from RA and OA control cases. This study identified six cell-type abundance phenotypes corresponding to distinct inflammatory states in RA that correlate with disease-relevant cell states, cytokines, risk genes, and serology metrics as described in Nature https://doi.org/10.1038/s41586-023-06708-y.
AMP RA/SLE Phase I CyTOF of PBMC samples profiling marker panels targeting T cells, B cells, and myeloid cells and total leukocyte (TL) samples profiling marker panels targeting TLs and PMN cells.
AMP RA/SLE Phase II CITE-seq experiment profiling PBMCs in two highly multiplexed experiments targeting either SLE and control cases or RA, RA at-risk, and control cases.
The Religious Orders Study (ROS) and Memory and Aging Project (MAP) are longitudinal clinical-pathologic cohort studies run by Rush University to investigate aging and Alzheimer's disease (AD). ROS enrolls individuals from religious communities across the U.S., while MAP recruits older adults from retirement communities in Illinois; both studies assess cognitive and motor function over time, diagnose AD using standardized methods, and conduct post-mortem neuropathologic evaluations to understand aging-related diseases.
These gene count TSV files represent gene expression data from various batches of human samples. They are associated with the Johns Hopkins NF1 biospecimen repository and include batch_1, batch2_addl, batch_2, batch_3, and mixed_batch. Researchers can employ RNA-seq analysis to investigate gene expression patterns, potentially identifying biomarkers, differential gene expression, and biological insights specific to each batch for diverse research purposes.
Single agent screen of the MIPE 4.0 library of approx. 1912 small molecules against 9 different cell-lines (5 NF1 nullizygous, 1 carrier, 2 normal, and 1 control) with diverse modes of action, and the generation of single agent viability results for each cell line to ID ~40 top hits (with highest potency and efficacy)
RNAseq data were generated from an Nf2fl/fl mouse model dorsal root ganglion tissue and cell line models of meningioma and schwannoma. In addition, data were generated from cell line models of meningioma and schwannoma with vehicle control, or 12 different single agent or combinations of small molecule inhibitors. This is data from the 2017 release.
Germline variants data processed from WGS data from the project Development of a Preclinical NF1-MPNST Platform Suitable for Precision Oncology Drug Discovery and Evaluation for the NF-OSI Processing Initiative
Execution of 6 x 6 screen of the top 40 compounds from initial screening, to elicit 780 combinations, such that the top 72 unique combinations (with preliminary optimal synergism profiles) can be elucidated
MS01 and MS11 mouse Schwann cells (NF2-/- and NF2 wild-type) were screened with 95 different drugs and vehicle conditions for 48 hours in an 8-point dose response format. The screen also included a 30 minute incubation wih 10uM EdU to assess DNA replication in all conditions. At the end of the incubation period, phenotypic measurements were performed with an automated microscope.
Processed gene expression profiles reflecting a human Schwann cell model for cNF and to identify differences in susceptibility to NF1 loss in different stages of Schwann cell development.
Germline variants data processed from WGS data from the project Ultra-low-pass whole genome sequencing of plasma cfDNA from patients with plexiform neurofibroma and malignant peripheral nerve sheath tumors for the NF-OSI Processing Initiative
Execution of 10 x 10 screen of top 72 compounds from 2nd screen, in order to focus on 9 combinations prioritized for validation in mouse NF1-/- primary Schwann cells
Germline variants data processed from WGS data from the project Targeting the mechanisms underlying cutaneous neurofibroma formation in NF1 - a clinical translational approach for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Ultra-low-pass whole genome sequencing of plasma cfDNA from patients with plexiform neurofibroma and malignant peripheral nerve sheath tumors for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Ultra-low-pass whole genome sequencing of plasma cfDNA from patients with plexiform neurofibroma and malignant peripheral nerve sheath tumors for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Ultra-low-pass whole genome sequencing of plasma cfDNA from patients with plexiform neurofibroma and malignant peripheral nerve sheath tumors for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Development of a Preclinical NF1-MPNST Platform Suitable for Precision Oncology Drug Discovery and Evaluation for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Development of a Preclinical NF1-MPNST Platform Suitable for Precision Oncology Drug Discovery and Evaluation for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Development of a Preclinical NF1-MPNST Platform Suitable for Precision Oncology Drug Discovery and Evaluation for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Targeting the mechanisms underlying cutaneous neurofibroma formation in NF1 - a clinical translational approach for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Targeting the mechanisms underlying cutaneous neurofibroma formation in NF1 - a clinical translational approach for the NF-OSI Processing Initiative
Germline variants data processed from WGS data from the project Targeting the mechanisms underlying cutaneous neurofibroma formation in NF1 - a clinical translational approach for the NF-OSI Processing Initiative
This study uses atomic force microscopy (AFM) to measure the the deflection of a cantilever upon contact with the cells. 30 cell lines were examined over 7 experimental conditions.
In this study, live cells were plated on fluorescent beads and fluorescently labeled with CellTracker Green CMFDA (Invitrogen) and DRAQ5 (Cell Signaling Technology) to label cytoplasm and cell nucleus respectively. 28 cell lines were examined.
This study uses images of cells collected using brightfield microscopy at 10x magnification, with ImageJ software used to trace the outline of single cells as well as to report area, circularity and aspect ratio. 30 cell lines were examined over 7 experimental conditions.
This study uses images of cells collected using brightfield microscopy at 10x magnification, with ImageJ software used to track motility. 30 cell lines were examined over 7 experimental conditions.
Region of interest annotations and whole slide scans at 40x magnification of Hematoxylin and Eosin stained liver tissue sections from male mice with human melanoma cell line xenografts
Region of interest annotations and whole slide scans at 40x magnification of Hematoxylin and Eosin stained brain tissue sections from male mice with human melanoma cell line xenografts
This study provides transcriptomic data from a samplw swap analysis done to identify technical artifacts across RNAseq datasets from the ROSMAP, MSBB, and Mayo RNAseq studies.
This study provides transcriptomic data from a variety of mouse models of AD and related dementias, and results of an analysis of how these models overlap with expression changes reported in human brains from individuals with AD.
This study provides proteomics data from the dorsolateral prefrontal cortex and precuneus from individuals from the Baltimore Longitudinal Study on Aging study.
The study provides transcriptomic data from monocytes taken from 5 healthy human subjects and differentiated into macrophages and microglia-like cells using polarizing cytokines.
This study provides imaging, laboratory and neuropsychological tests, metabolomics, proteomics, plasma biomarkers, and genomic variant data and on a cohort of middle aged individuals with no cognitive impairment.
This study provides proteomics data from cultured neurons from rats transduced with lentivirus to overexpress: APP.PS1; APP.PS1 and mutant or wildtype U1-70; mutant or wildtype U1-70.
This study provides transcriptomic and genomic data from the dorsolateral prefrontal cortex from individuals from the Harvard Brain Tissue Research Center.
This study provides genomic, transcriptomic, and immunoassay data from the cerebellum and temporal cortex from individuals with a neuropathological diagnosis of AD, with or without cerebral amyloid angiopathy (CAA) pathology.
This study provides genomic, transcriptomic, and proteomic data from the cerebellum and temporal cortex from individuals from the Mayo Clinic Brain Bank and Banner Sun Health Research Institute.
This study provides transcriptiptomics data from 19 brain regions from individuals from the Mount Sinai/JJ Peters VA Medical Center Brain Bank collection.
This study provides genomic, transcriptomic, epigenomic and proteomic data from multiple brain regions of individuals from the Mount Sinai/JJ Peters VA Medical Center Brain Bank collection.
This pilot study provides proteomic data from brain tissue obtained from the autopsy collections of the University of Pennsylvania School of Medicine Brain Bank.
This study provides behavioral, electrophysiology, and imaging data on a variety of diabetic and amyloidogenic mice with and without transient occlusion of the middle cerebral artery.
This study provides metabolomics data from serum from indivuduals from the Penn Memory Center, Alzheimer's Disease Clinical Center and Maria de los Santos Health Center .
This study provides single-cell transcriptomic data from the prefrontal cortex from individuals sleceted from the Religious Orders Study and Memory and Aging Project (ROSMAP).
This study provides transcriptomic, metabolomic, and imaging data on individuals participating in a non-interventional cohort study conducted at Emory University.
This study provides proteomics data from brain tissue obtained from the autopsy collections of the University of Pennsylvania School of Medicine Brain Bank.
This study provides single-nucleus transcriptomic data from the prefrontal cortex from individuals with TREM2 variants selected from the the Religious Orders Study and Memory and Aging Project (ROSMAP)
This study provides proteomics data on brain tissue, serum, and cerebrospinal fluid obtained from donor tissue from the Banner Sun Health Research Institute.
This study provides transcriptomic data from PAXgene blood samples of participants from an antemortem, prospective, population-based cohort of European descent.
This study provides transcriptomics data from the prefrontal cortex, the entorhinal cortex, and the dentate gyrus of APP/PSEN1 tarnsgenic mice with or without a constitutive deletion of miR155.
This study provides details about analyses performed by the Icahn School of Medicine at Mount Sinai AMP-AD team that led to a set of nominated targets in Agora.
This study provides single cell transcriptomic data from individuals selected from the Religious Orders Study and Memory and Aging Project (ROSMAP) and wild-type mice.
This study provides longitudinal metabolomics data generated on the Nightingale Health Platform from serum from the Alzheimer's Disease Neuroimaging Initiative - 1, GO, and 2 cohorts.
This study provides bulk RNA sequencing data and quantitative proteomics data associated with two projects examining cognitive resilience to Alzheimer’s disease, using samples from two longitudinal studies of aging - the Religious Orders Study and the Memory and Aging Project (ROSMAP).
This study provides proteomics data from the frontal cortex and anterior cingulate cortex from individuals from the Emory Alzheimer’s Disease Research Center
This study provides data mining analysis files generated during the development of the MindDiseasePhenome and MindDrugPhenome knowledge bases from 30 million biomedical publications.
This study provides label-free proteomics and metabolomics data from brain homogenates and serum of APOE4.Trem2*R47H and 5XFAD mouse models of late-onset Alzheimer's disease.
This study provides metabolomics data on serum from the ADNI 1, GO, and 2 cohorts using the Baker Lipidomics platform. The data was generated from samples collected at the baseline visit.
This study provides cell-type specific transcriptomic and epigenetic data from multiple brain tissues of 10 neurotypical individuals belonging to the Mount Sinai Brain Bank cohort.
This study provides mitochondrial DNA variants and mtDNA copy number estimates generated using whole genome sequencing data obtained from multiple brain tissues as part of the ROSMAP, MayoRNASeq, and MSBB studies.
This study provides immunoassay (targeted proteomics), untargeted metabolomic, and genomic variant data from 472 adults with Down Syndrome, in conjunction with direct neuropsychological testing and structured informant interviews regarding daily functioning and psychiatric symptoms.
This study provides whole transcriptome and proteomic data for iPSC derived neurons from a curated set of "Religious Order Study" (ROS) and "Memory and Aging Project" (MAP) subjects across a spectrum of Alzheimer’s Disease (AD) pathologies.
This study provides targeted bisulfite sequencing data from brain tissue obtained from 150 randomly selected participants from the ROSMAP cohort, and the results of Expression Wide Association Study (EWAS) analyses between expression data and six AD-related traits.
This study provides RNAseq data from lymphoblastoid cell lines selected for carriage of mitochondrial variants that have emerged from analysis of AMP-AD mitochondrial data.
This study provides RNAseq, ATACseq, HiC, and SNP array data on microglia isolated from fresh autopsy and biopsy specimens taken from individuals in the ROSMAP cohort, the Mount Sinai/JJ Peters VA Medical Center NIH Brain and Tissue Repository, and the Living Brain Project.
This study provides uniformly processed mitochondrial genome variant calls based on whole genome sequencing data from 1881 individuals profiled through the ROSMAP, MSBB, and MayoRNAseq studies.
This study provides lipidomics data on human pre-mortem plasma samples (n = 674) and post-mortem brain tissue (n = 384) from Religious Order Study (ROS)/Memory and Aging Project (MAP) participants.
This study provides methylation array data from brain tissue belonging to donors in the Religious Orders Study (ROS) and Memory and Aging Project (MAP) cohorts. The individuals included in this study represent the full spectrum of Alzheimer's disease severity, but were selected in a manner designed to enrich the proportion of APOE e4 carrying individuals.
This study is a release of RNA sequencing data from the ROSMAP, MSBB, and MayoRNAseq studies that has been processed using a common workflow. The study is an extension of the rnaSeqReprocessing study, and has data from donors that are also part of the WGS_Harmonization study. RNAseq data in this study has been aligned to the GRCh38 reference genome.
This study provides long read whole-genome sequencing data generated on the PacBio platform for two ROSMAP individuals; structural variant calls generated from existing short-read WGS data available on 1760 individuals from the ROSMAP, MSBB, and MayoRNASeq studies; and summary results from eQTL, pQTL, haQTL, and sQTL analyses.
This study aims to identify microglial transcriptomic signatures in neurosurgical tissue. Fresh brain tissue was obtained from 25 unique patients undergoing neurosurgical procedures for epilepsy or tumor resection. Transcriptome measures were captured for bulk brain tissue, bulk population of sorted microglia, and single cells from sorted microglial population.
This study provides transcriptomic and chromatin accessibility data from single nuclei isolated from brain tissue of 84 aged individuals spanning the full spectrum of Alzheimer's disease severity and 5 neurotypical adult reference individuals, as well as genotype data for those individuals.
This study provides bulk brain RNAseq and single-cell RNAseq data from Plxnb1 knockout (KO) mice (C57BL/6J background) which were crossed with APP/PS1 transgenic mice or TAU (TAU-PS19) transgenic mice.
This study provides bulk RNAseq data from prefrontal cortex samples from a living brain cohort matched for age and sex to a postmortem brain cohort. The living samples were collected from individuals undergoing a deep brain stimulation electrode implantation surgery. A total of 535 brain samples were collected from 417 individuals (171 living and 246 postmortem).
This study provides bulk RNAseq data from the hippocampus of 40 donors with Alzheimer's disease and 15 nondemented controls from the Mayo Clinic Brain Bank.
This study provides whole genome sequence data from patients diagnosed with Alzheimer's disease and frontotemporal dementia at the University of California, San Francisco Memory and Aging Center. WGS data were generated from pre-mortem blood samples taken from 317 AD cases, 347 FTLD cases, and 102 controls.
This study provides gene expression and proteomic data from fruit fly models of neurodegenerative disease (Alzheimer’s, Parkinson’s, and Huntington’s diseases).
This study provides data on gut microbial metabolites, including bile acids, from serum samples taken from participants in the ADNI 1, GO, and 2 human cohorts. Quantitative measurement of these samples was carried out using ultra-performance liquid chromatography coupled to tandem mass spectrometry at the University of Hawaii.
This study provides genome-wide histone 3 lysine 27 acetylation (H3K27ac) profiles of three major cell types from 16 hippocampus samples and 10 dorsolateral prefrontal cortex samples obtained from ROSMAP subjects with and without Alzheimer’s Disease.
This study provides DNA methylation array data for Alzheimer’s disease (AD) and non-demented control dorsolateral prefrontal cortex (DLPFC) brain samples from 223 donors, which were obtained from the University of Pittsburgh Alzheimer’s Disease Research Center (PITT-ADRC).
This study provides single-nucleus RNA sequencing (snRNAseq) data obtained from the temporal cortex (TCX) of 36 individuals with a diagnosis of progressive supranuclear palsy (PSP) or controls.
A randomized, double-blind, cross-over, single-center pilot study of MMKD (Modified Mediterranean Ketogenic Diet) versus American Heart Association Diet (AHAD) intervention performed on 17 subjects (age: 64.6 ± 6.4 yr), of which 11 have mild cognitive impairment (MCI), while 6 are cognitively normal.
This study provides single-nucleus RNAseq profiles from the dorsolateral prefrontal cortex of 1494 donors from the Mt Sinai Brain Bank, NIMH Human Brain Collection Core, and ROSMAP cohorts. In addition to Alzheimer's Disease status, information on the presence of other dementias or neuropsychiatric conditions is also provided.
This study provides single-nucleus transcriptomic data from the temporal cortex of 24 subjects from the Mayo Clinic Brain Bank, with the aim to identify vascular biomarkers that are associated with neuropathological diagnosis, neuropathology scores, risk factors such as age, sex, and APOE genotype.
This study uses human induced pluripotent stem cells (hiPSCs) along with CRISPR-Cas9 gene editing to investigate the contribution of chromosome 21 candidate genes to AD-relevant neuronal phenotypes.
This study evaluates the utility of human induced pluripotent stem cell-derived neurons and astrocytes as tools to systematically test AD-relevant cellular phenotypes following perturbation of candidate genes identified by genome-wide studies.
This study establishes an experimental system that integrates genetic information with a heterogeneous set of iPSCs to identify genetic contributions to molecular pathways affecting AD risk and resilience.
This study provides measurements of the levels of selected metabolites in 4891 human serum samples (2603 for ADNI-1, 2288 for ADNI-GO/2) using the Biocrates MxP® Quant 500 kit.
This study validates and extends the clinical research findings from the Alzheimer’s Gut Microbiome Project (AGMP) by employing preclinical animal models where experimental variables can be rigorously controlled, unlike in human studies.
This study uses different model systems including HMC3 cells, iPSC-derived microglia and cerebral organoids to characterize the effect of two topoisomerase I inhibitors in mimicking this human microglial subtype in vitro.
Using data from the AMP RA.SLE Phase II PBMC CITE-seq and AMP RA.SLE PhaseII CyTOF datasets, investigators examined PBMC gene and protein expression patterns and systematically identified activated lymphocyte phenotypes in RA At-Risk individuals, along with immunophenotypic differences between different At-Risk subpopulations
Using data from the AMP RA Immune Repertoire Profiling dataset, synovial tissue and synovial fluid CD8+ T cells were found to be predominated by a population of effector CD8+ T cells characterized by high expression of granzyme K and low expression of granzyme B and perforin as described in Science Translational Medicine https://doi.org/10.1126/scitranslmed.abo0686.
Using data from the AMP RA Immune Repertoire Profiling dataset, this study identified clonal relationships between functionally distinct lymphocyte populations that infiltrate the synovium of patients with RA as described in Nature Communications https://doi.org/10.1038/s41467-024-49186-0.
Using data from the AMP RA.SLE PhaseII CyTOF dataset, investigators evaluated the heterogeneity of immune activation in patients with lupus nephritis to identify correlates of renal parameters and treatment response.
AMP RA Phase II unimodal 10x Genomics Epi ATAC open chromatin profiling of disaggregated synovium samples from 18 rheumatoid arthritis and osteoarthritis cases.
AMP SLE Phase II kidney scRNA-seq data was used to compared intrarenal myeloid cells in four mouse models and 155 lupus nephritis patients. The authors identified analogous disease-associated monocytes and macrophages between humans and mice that were associated with kidney histological subtypes and disease progression, sharing gene expression and localizing to similar kidney microenvironments as in mice. This cross-species analysis supports the use of mouse functional studies for understanding human lupus nephritis.
Latest release of the data within GENIE shared with the global research community. The database currently contains CLIA-/ISO-certified genomic data obtained during the course of routine practice at multiple international institutions
This synthetic dataset of 19,859 participants was generated using a transformer-based model trained on data from 4, 203 individuals in the New England Centenarian Study. It includes demographics, clinical outcomes, physical assessments, genotype, proteomics, and metabolomics. Created by Syntegra Inc. in 2022, the dataset was cleaned for consistency and supports research on aging and longevity.
This study investigates the molecular mechanisms of longevity in birds by analyzing transcriptomic, proteomic, and metabolomic data across multiple tissues to identify key gene expression biomarkers linked to lifespan. By comparing these longevity signatures to those previously identified in mammals, the research aims to uncover both universal and species-specific pathways that regulate lifespan across vertebrates, potentially informing future lifespan-extending interventions.
This study includes transcriptomics data of 399 blood samples from participants enrolled in the ILO project Identifying protective omics profiles in centenarians and translating these into preventive and therapeutic strategies.
This study investigates the effects of five longevity-enhancing interventions on 12-month-old UM-HET3 mice compared to untreated controls and young (4-month-old) mice. The primary objective is to identify metabolomic differences across six organs to understand how these interventions influence metabolic pathways associated with aging and extended longevity.
The study provides data from 209 samples including 78 centenarian samples (over 100 years of age) and 131 younger samples (59-99). The samples were collected as part of the Integrative longevity Omics (ILO) study. DNA extraction and shotgun metagenomics sequencing were performed on the samples for taxonomic profiling.
The study investigated the cell type-specific mechanisms involved in Alzheimer's disease (AD) through the development of 3D cerebral organoid-based models of the disease exploiting well-established isogenic hiPSC carrying heterozygous familial AD mutations (PSEN1M146V and APPswe).
The Characterization of gene associations with aging-related traits with a genetically-predicted transcriptome-wide association study (ADAMTS7) provides analyses of candidate genes and the association of Longevity-Associated Variants (LAVs) with aging-related traits and diseases.
This study provides analysis results of a two Sample Mendelian Randomization used to analyze the relationship between significantly associated GWAS traits and five distinct definitions of longevity.
This study is a collection of genetically-predicted tissue-specific gene expression associations with a collection of aging-related traits and outcomes.
This study features an investigation of human longevity using metabolomics and proteomics, data collected through a case-cohort design. Longevity cases were defined as individuals who lived longer than 98% of their peers, based on U.S. life expectancy data. Participants came from four long-term studies of older adults—MrOS, SOF, Health ABC, and CHS. A random sample of participants was selected for comparison, including some who also reached exceptional ages.