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1,921 results for “single cell analysis”
Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma
<p>Here, we performed an integrative analysis of scRNA-seq and scATAC-seq data from four ccRCC patients and aimed to identify the key regulatory molecules that mediate tumor development and manipulate the function of immune cells.</p>
RNA velocity analysis of the integrated single cell atlas of neural crest lineages along the posterior developing zebrafish
<p>H5AD files of an RNA velocity analysis of the integrated single cell atlas of neural crest lineages along the posterior developing zebrafish . For this, we have used Velocyto and scVelo. The notebooks to reproduce the scVelo part are here https://github.com/brunicardoso/e-signal-lab/blob/main/scvelo_sox10_integration48_68h__Uribe_using_original_seurat_metadata.ipynb .</p> <p>This analysis was based on data published here https://elifesciences.org/articles/60005</p>
Single Cell Analysis of the Pathogenesis of Pediatric Nephrotic Syndrome
<p>This is ScRNAseq datasets used to analyses the pathogenesis of nephrotic syndrome. </p>
AnnData set for single cell analysis tutorial
Open the record for dataset details and reuse information.
Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease (Invitro ArchR Object)
<p>This repo contains invitro ArchR object</p>
Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease (Invivo ArchR Object)
<p>This repo contains invivo ArchR object</p>
Cellular and molecular heterogeneities and signatures, and pathological trajectories of fatal COVID-19 lungs defined by spatial single-cell transcriptome analysis
<p>Spatial in-situ data analysis.</p>
Single cell spatial analysis and biomarker discovery in Hodgkin lymphoma
<p>Imaging Mass Cytometry Data of Hodgkin Lymphoma. Details in associated manuscript</p>
BRACE: A Bayesian-based dimension reduction approach for single-cell alternative splicing analysis
<p>Datasets to demonstrate the utility of our BRACE method.</p>
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
<p>Collection of auxiliary data to reproduce the results from "Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease".</p> <p>Source code is available at: https://github.com/saezlab/MOFAcell</p> <p>Exceptions: Spatial data is excluded</p> <p>This folder contains processed data of the following publications, when using the data cite accordingly:<br> 1) Kuppe C, Ramirez Flores RO, Li Z, Hayat S, Levinson RT, Liao X, Hannani MT, Tanevski J, Wünnemann F, Nagai JS, et al (2022) Spatial multi-omic map of human myocardial infarction. Nature 608: 766–777<br> 2) Ramirez Flores RO, Lanzer JD, Holland CH, Leuschner F, Most P, Schultz J-H, Levinson RT & Saez-Rodriguez J (2021) Consensus Transcriptional Landscape of Human End-Stage Heart Failure. J Am Heart Assoc 10: e019667<br> 3) Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, et al (2022) Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science 377: eabo1984<br> 4) Chaffin M, Papangeli I, Simonson B, Akkad A-D, Hill MC, Arduini A, Fleming SJ, Melanson M, Hayat S, Kost-Alimova M, et al (2022) Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy. Nature 608: 174–180 </p>
Data accompanying "Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using the scp package"
<p>Data and scripts accompanying the paper <em>Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using scp</em>.</p> <ul> <li>d.zip contains raw MS data from samples run on timsTOF SCP.</li> <li>raw.zip contains raw MS data from samples run on orbitrap mass spectrometers (Orbitrap Fusion Lumos Tribrid and Exploris 240).</li> <li>mzML.zip contains raw MS data in mzML format from all samples.</li> <li>sage.zip contains output results from the sage software (results.sage.tsv and quant.tsv) as well as configuration files (results.json) for both orbitrap (cbio) and timsTOF (giga) data.</li> <li>sample_annotation.zip contains csv files with samples annotation for each acquisition batch and used to build the colData.</li> <li>example_subset.zip contains csv files for short example datasets displayed in the paper.</li> <li>scp.rds file contains the initial QFeatures object of the full dataset with 56 PSM sets corresponding to the 56 MS runs.</li> <li>build_QF_dataset.Rmd file is the script used to build the scp.rds file described above from sage outputs and sample annotation.</li> </ul> <p>These file descriptions are also available in the README.txt file.</p>
GO Enrichment Analysis on Single-Cell RNA-Seq Data
Open the record for dataset details and reuse information.
Single-Cell and Spatial Transcriptomics Analysis of Steatotic Donor Liver Susceptibility to Post-Transplant Injury
ClinicalTrials.gov study NCT07362745. IPD Sharing: NO. Countries: 1. Publications: 0.
Analysis of single cell gene expression profile in hiPSC-derived NPCs
GEO Series GSE151642. Homo sapiens. 96 samples. Type: Expression profiling by high throughput sequencing; Other.
Single-cell transcriptional analysis of human pluripotent stem cell-derived heart epicardium-myocardium organoids uncover principals of human epicardial-derived cells specification and coronary vascul
GEO Series GSE309829. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Decoding Dengue's Neurological Assault: Insights from Single-Cell CNS Analysis in a Mouse Model
GEO Series GSE252515. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Single-cell and single-nucleus transcriptome analysis of pattern formation in the early embryo of the spider Parasteatoda tepidariorum
GEO Series GSE201705. Parasteatoda tepidariorum. 3 samples. Type: Expression profiling by high throughput sequencing.
Identification of human tumor-unique signaling networks between antigen-presenting cells and T cells using multi-omic single cell analysis
GEO Series GSE163633. Homo sapiens. 131 samples. Type: Expression profiling by high throughput sequencing.
Drop-seq analysis of bleomycin-treated and control mouse lung single-cell suspensions
GEO Series GSE111664. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains
GEO Series GSE202210. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
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.