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1,237 results for “cell characterization”
Data from: Non-invasive stratification of non-alcoholic fatty liver disease by whole-transcriptome cell-free mRNA characterization
<p>Hepatic fibrosis stage is the most important determinant of outcomes in patients with non-alcoholic fatty liver disease (NAFLD). There is an urgent need for non-invasive tests that can accurately stage fibrosis and determine efficacy of interventions. Here we describe a novel cf-mRNA-Sequencing approach that can accurately and reproducibly profile low levels of circulating mRNAs and evaluate the feasibility of developing a cf-mRNA-based NAFLD fibrosis classifier. Using separate discovery and validation cohorts with biopsy-confirmed NAFLD (n=176 and 59, respectively) and healthy subjects (n=23), we performed serum cf-mRNA RNA-Seq profiling. Differential expression analysis identified 2498 dysregulated genes between NAFLD and healthy subjects and 134 fibrosis-associated genes in NAFLD patients. Comparison between cf-mRNA and liver tissues transcripts revealed significant overlap of fibrosis associated genes and pathways indicating that the circulating cf-mRNA transcriptome reflects molecular changes in the livers of NAFLD patients. In particular, metabolic and immune pathways reflective of known underlying steatosis and inflammation were highly dysregulated in the cf-mRNA profile of patients with advanced fibrosis. Finally, we used an elastic net ordinal logistic model to develop a classifier that predicts clinically significant fibrosis (F2-4). In an independent cohort, the cf-mRNA classifier was able to identify 50% of patients with at least 90% probability of clinically significant fibrosis. We demonstrate<b> </b>a<b> </b>novel and robust cf-mRNA-based RNA-Seq platform for non-invasive identification of diverse hepatic molecular disruptions and for fibrosis staging with promising potential for clinical trials and clinical practice.</p>
Yeast cell-based transport assay for the functional characterization of human 4F2hc-LAT1 and ‐LAT2, and LAT1 and LAT2 substrates and inhibitors
<p>Data to Kantipudi & Fotiadis (2021), <em>Front. Mol. Biosci. </em>(2021) <strong>8</strong>, 676854.</p>
A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma
<p>This repository contains R Seurat objects associated with our study titled "<strong>A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma</strong>". </p> <p>This repository contains two Seurat objects stored in .rds files containing processed single-cell RNA sequencing data from the original ‘Discovery’ cohort of the MMRF Immune Atlas study, along with an additional ‘Discovery + Validation’ cohort, as described in the original publication. These .rds files contain Seurat v4 objects with basic cell type annotation and qc metadata. Specific file contents will be detailed below.</p> <div> <p>A copy of the ‘Cell Annotation Dictionary’ is also included, which contains additional details on the individual annotated clusters in the Immune Atlas dataset.</p> <p>Information on how to request additional metadata about these samples and accessing the original fastq files will be detailed at the end of this description</p> </div>
CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators (PBMC data)
<p>This site provides access to datasets from the CPA-Perturb-seq manuscript Kowalski*, Wessels*, Linder* et al., including PBMC data to replicate analyses in Figure 6. We release these data as Seurat objects, where each object contains single-cell quantifications of gene expression (RNA assay), and in addition, quantifications of polyA site usage (polyA site assay). To explore these data, please install the <a href="https://github.com/satijalab/PASTA">PASTA</a> (PolyA Site analysis using relative Transcript Abundance) package which provides infrastructure and analytical tools to explore alternative polyadenylation at single-cell resolution. For each dataset, we also include a fragment file which enables visualization of read coverage plots across groups of cells. </p> <p> </p> <p>To replicate the analysis in Figure 6, in which we analyze a dataset of circulating human peripheral blood mononuclear cells, we provide a vignette available <a href="http://www.satijalab.org/seurat/articles/pasta_vignette.html">here</a>. To following files are used:</p> <p> </p> <ol> <li> <p>matrix.mtx: 10X file containing RNA for PBMC dataset</p> </li> <li> <p>barcodes.tsv: 10X file containing barcodes for PBMC dataset</p> </li> <li> <p>genes.tsv: 10X file containing genes for PBMC dataset</p> </li> <li> <p>PBMC_meta_data.csv: meta data for PBMC dataset</p> </li> <li> <p>PBMC_pA_counts.tab.gz: Counts file containing polyA quantification for PBMC dataset</p> </li> <li> <p>PBMC_fragments.tsv.gz: Fragment file to visualize the PBMC dataset.</p> </li> <li> <p>PBMC_fragments.tsv.gz.tbi: Fragment file index for the PBMC dataset. </p> </li> <li> <p>PBMC_polyA_peaks.gff: Gff file containing location of polyA site read regions.</p> </li> <li> <p>human_PAS_hg38.txt: Text file containing information from polyAdbv3 resource. </p> </li> </ol>
Replicative senescence in human embryo bone marrow MSCs is characterized by changes in cell motility and subcellular local-ization of Rac1 and RhoA GTPases
<p>Supplementary files to the article "Replicative senescence in human embryo bone marrow MSCs is characterized by changes in cell motility and subcellular local-ization of Rac1 and RhoA GTPases"</p>
Real Time Molecular Characterization of Diffuse Large B Cell Lymphoma (DLBCL)
ClinicalTrials.gov study NCT03104478. IPD Sharing: NO. Countries: 1. Publications: 0.
Molecular-genetic Characterization in Patients Undergoing CAR-T Cell Infusion
ClinicalTrials.gov study NCT05807789. IPD Sharing: YES. Countries: 1. Publications: 0.
Characterization of Pulmonary Langerhans Cell Histiocytosis
ClinicalTrials.gov study NCT03093727. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Exploratory Study of Molecular Characterization in Patients With Metastatic Germ Cell Tumours Refractory/Resistant to Platinum Treatment
ClinicalTrials.gov study NCT03980587. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Multiple Myeloma is a Hematologic Malignancy Characterized by the Accumulation of Malignant Plasma Cells in the Bone Marrow. Despite Advances in Treatment, Many Patients Experience Disease Relapse. Bi
ClinicalTrials.gov study NCT06888856. IPD Sharing: NO. Countries: 0. Publications: 0.
Characterization of Methylation Pattern in Human Germ Cells of Patients Undergoing ICSI Treatment
ClinicalTrials.gov study NCT03565107. IPD Sharing: NO. Countries: 1. Publications: 0.
Characterization of Adipose Derived Regenerative Cells (ADRCs) From Patients With Chronic Heart Disease
ClinicalTrials.gov study NCT02732106. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Collection of Blood and/or Bone Marrow for Investigation and Characterization of Normal and Abnormal Cell Growth
ClinicalTrials.gov study NCT01174615. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Characterization of Biliary Cell-derived Organoids from Bile of PSC and Non-PSC Patients
ClinicalTrials.gov study NCT04753996. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Molecular Characterization of Perivascular Epithelioid Cell Tumors
ClinicalTrials.gov study NCT05617105. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Characterization of Ovarian Cancer Stem Cell
ClinicalTrials.gov study NCT01367353. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Characterization of Natural Killer Cells in Severe Asthma Patients in Comparison With Control Subjects
ClinicalTrials.gov study NCT06015256. IPD Sharing: NO. Countries: 1. Publications: 0.
Characterization of the Microbiome in Cutaneous T Cell Lymphoma
ClinicalTrials.gov study NCT03932279. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Measurement and Characterization of Circulating Endothelial Cells or Circulating Tumor Cells or Circulating DNA in Adult Patients With Metastatic Cancer
ClinicalTrials.gov study NCT02666612. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Characterization of Beta Cell Failure
ClinicalTrials.gov study NCT00869102. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.