Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
11,105
datasets available to search
ShareScore release 0.9.0
Dataset results
11,105 results for “single cells”
STING OPS: HeLa Genome-wide Screen Single-Cell Features (Part 3/5)
<div> <div> <p><strong>Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening</strong></p> <p>Single-cell features and coordinates for HeLa genome-wide screen, Zenodo dataset part 3/5.</p> <p>Images available at gs://opspublic-east1/STINGOpticalPooledScreen/Images/GW*.</p> <p>README for additional image information is at gs://opspublic-east1/STINGOpticalPooledScreen/STING_README.</p> </div> </div>
STING OPS: HeLa Genome-wide Screen Single-Cell Features (Part 4/5)
<div> <div> <p><strong>Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening</strong></p> <p>Single-cell features and coordinates for HeLa genome-wide screen, Zenodo dataset part 4/5.</p> <p>Images available at gs://opspublic-east1/STINGOpticalPooledScreen/Images/GW*.</p> <p>README for additional image information is at gs://opspublic-east1/STINGOpticalPooledScreen/STING_README.</p> </div> </div>
Data for Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data
<p>This is the accompanying data to the manuscript titled<em> Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data</em>. To reproduce the TRIBAL output please use this <a href="https://doi.org/10.5281/zenodo.12741290">code repository</a> as the arguments and codebase may have changed since release. </p>
Single-cell analyses of polyclonal Plasmodium vivax infections and their consequences on parasite transmission Source Data
<p>Source Data for the paper by Hazzard et al. entitled <em>Single-cell analyses of polyclonal Plasmodium vivax infections and their consequences on parasite transmission</em>.</p>
Mass spectra for single Scrippsiella trochoidea cells: light vs. dark & replete vs. N limiting conditions
<p>Data files for 77 <em>Scrippsiella trochoidea </em>cells measured in single cell MS experiments. Information about the experimental conditions, corresponding file names, the number of cells for which data are recorded in each respective file, and the range of acquisition times for individual cells can be found in the supplemental documentation of the corresponding manuscript titled : "Single Cell Metabolomic Analysis of <em>Scrippsiella trochoidea</em>" in Frontiers in Plant Science. </p> <p>Note: .mzML is a standard MS file format that can be viewed using freeware such as mMass (<a href="http://www.mmass.org/">http://www.mmass.org/</a>) and ProteoWizard (<a href="http://proteowizard.sourceforge.net/index.shtml">http://proteowizard.sourceforge.net/index.shtml</a>).</p> <p> </p> <p> </p> <p> </p>
Single-particle tracking data for "CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning"
<p>This dataset contains all the raw SPT data reported in "­­­­CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning" in the form of SPT trajectories. The SPT trajectories are provided in two different formats for convenience: a CSV format and a Matlab format. Both formats are readable by Spot-On: https://spoton.berkeley.edu/</p> <p>The SPT data contains "fast tracking" spaSPT data and this data was analyzed using the Matlab version of Spot-On which can be found and downloaded at: https://gitlab.com/tjian-darzacq-lab/spot-on-matlab</p> <p> </p> <p>Full details about the Matlab and CSV formats are provided in the ReadMe files in the associated zip files.</p> <p>Please see the associated manuscript for a detailed description of how the data was acquired and analyzed.</p>
Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries
<p>Processed data files for manuscript: "Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries" <a href="https://doi.org/10.1093/nar/gky1204">https://doi.org/10.1093/nar/gky1204</a> . Scripts for generating figures are found here: https://github.com/rnabioco/scrna-subsets</p>
Data for 'Comparative Analysis of Single-Cell RNA Sequencing Methods'
<p>Raw sequencing data to "Comparative Analysis of Single-Cell RNA Sequencing Methods". </p> <p>https://www.ncbi.nlm.nih.gov/pubmed/28212749</p> <p> </p> <p>In addition to the GEO submission https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75790, you can find here raw bam files for UMI-methods tagged with cell barcode and UMI sequences.</p> <p>MD5 checksum: f10825509952fffd9c4dc0c1dcb9eb8e</p>
Ensemble and single cell data for primary Ovis Aries pulmonary artery endothelial cells response to IGF-1 administration
<p>Data for IGF-1 administration of healthy and persistent pulmonary hypertension of the newborn primary Ovis Aries pulmonary artery endothelial cells.</p> <p>Ensemble.zip:<br> Dose-response to IGF-1<br> Proliferation<br> Western blots for VEGF and eNOS<br> IGF-1R and mTOR inhibition<br> Branch points in tube formation assay<br> <br> IF.zip:<br> Cellprofiler 3.1 analysis of snapshot data for the time course of IGF-1 administration with nuclei, actin, VEGF, and eNOS</p> <p>Translation.zip:<br> CellProfiler 3.1 analysis of snapshot data for the time course of IGF-1 administration with nuclei and total protein production</p>
Time-resolved single-cell RNA-seq using scSLAM-seq and GRAND-SLAM
<p>This is the example data for the protocol "Time-resolved single-cell RNA-seq using scSLAM-seq and GRAND-SLAM".</p> <p>The test data comprises sequencing data from 12 different cells. Five of them in mock condition with 4sU, five infected with MCMV with 4sU and 2 uninfected cells without 4sU. For each sample, paired-end sequencing was conducted and therefore two files exist for each sample. The files can be found at data/fastq.</p> <p>The reads should be mapped against the mouse genome and the MCMV genome, which are located in data/genome. The sequence is in fasta-fomat and the features in gtf-format.The scripts conducting quality control, read mapping and GRAND-SLAM analysis can be found in the processing folder. For each computational step in this protocol there is a shell script for running the necessary steps. Executing all scripts will reproduce the analysis of our test data</p>
Numbers of Single-Cell β-Actins
<p>The dataset is an Excel composed of ten columns representing absolute numbers of single-cell β-actins from cell types of A549 (column A, N<sub>cell</sub> = 14,242), Hep G2 (column B, N<sub>cell</sub> = 35,932), MCF 10A (column C, N<sub>cell</sub> = 16,650), HeLa (column D, N<sub>cell</sub> = 26,151), PC3 (column E, N<sub>cell</sub> = 11,922), SACC-83 (column F, N<sub>cell</sub> = 13,616), CAL 27 (column G, N<sub>cell</sub> = 7,271), CAL 27-LN2 (column H, N<sub>cell</sub> = 6,222), Oral Tumour Patient I (column I, N<sub>cell</sub> = 359) and Oral Tumour Patient II (column J, N<sub>cell</sub> = 175), respectively.</p>
Single-cell Hi-C matrix Nagano 2017
<p>Single-cell Hi-C interaction matrix in mcool format, provided in 10kb and 1Mb. Data based on Nagano 2017: Cell-cycle dynamics of chromosomal organization at single-cell resolution</p>
scDenorm: a denormalisation tool for Integrating Single-cell Transcriptomics Data
<p>Datasets and Jupyter notebooks to reproduce the analyses presented in the manuscript, scDenorm: a denormalisation tool for Integrating Single-cell Transcriptomics Data.</p>
Chronic social defeat stress induces meningeal neutrophilia via type I interferon signaling: single cell RNA sequencing data
<p>Meningeal single cell RNA sequencing data</p> <p>Meningeal samples were collected from both dorsal and ventral skull, avoiding inclusion of choroid plexus. Samples were digested in 2.5 mg/mL Collagenase D (Cat. #11088858001; Roche) and 12.5 μL of 0.5 mg/mL DNAseI (Cat. #L5002139; Worthington), put on a shaker at 370C for 30 m, diluted with cold HBSS + 0.1% BSA, and mashed through a 70 μm cell strainer prior to sorting.</p> <p>Data represent live, nucleated, singlet cells (DAPI-DRAQ5+) sorted on a BD FACS Aria Fusion into HBSS + 10% FBS prior to droplet encapsulation using 10x Genomics’ Drop-seq platform (Chromium v2).</p> <p>10X chip lane is indicate by 'group' column</p> <p>Group 1 = 4 pooled homecage control (unstressed) mice</p> <p>Group 2 = 4 pooled homecage control (unstressed) mice</p> <p>Group 3 = 4 pooled mice exposed to chronic social defeat for 14 days; tissue was collected 2 hours following final defeat</p> <p>See the following repositories for data processing:</p> <p><a href="https://github.com/maryellenlynall/2019_bcell_stress/blob/master/bcellstress20.Rmd">https://github.com/maryellenlynall/2019_bcell_stress/</a> (processing from raw files starts at bcellstress020.Rmd)</p> <p><a href="https://github.com/staceykigar/meningeal_neut/">https://github.com/staceykigar/meningeal_neut/</a></p> <p>We also provide a processed dataset (processed.RData) with assays 'counts' and 'logcounts' which is the processed single cell object saved at line "# Save object for upload to Zenodo" in script <a href="https://github.com/staceykigar/meningeal_neut/">https://github.com/staceykigar/meningeal_neut/</a>neutrophilstress01.Rmd </p> <p>Cluster annotations are in sce$Annotation</p> <p>Neutrophil subcluster annotations are in sce$Subcluster</p> <p>Sample condition is in sce$cond, where "HC" indicates homecage control and "SD" indicates chronic social defeat</p> <p>10X chip lane is in sce$group</p>
Single-cell embryo dataset for X-scPAE
<p>The E-MTAB-3929 dataset is a human embryo dataset that includes 1,096 samples from three developmental stages: day 5 (E5), day 6 (E6), and day 7 (E7) of embryonic development. These samples belong to three cell lineages: PE, TE, and EPI, with 11,662 gene features.</p> <p>The GSE36552 dataset is a human embryo dataset that includes 66 samples from the 8-cell stage, morula stage, and late blastocyst, with 15,143 gene features.</p> <p>The GSE109071 dataset is a mouse embryo dataset that includes 1,724 samples from embryonic developmental stages E5.25, E5.5, E6.25, and E6.5, with 7,565 gene features.</p>
Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplicatively
<p>This repository contains simulated data generated with GLiMMIRS-sim that was analyzed and presented in Zhou & Guyuvayurappan et al, as well as data pertaining to the <em>NMU</em> RT-qPCR experiment described in the manuscript. </p> <p> </p> <ul> <li><span>sim_base_data.tar.gz: directory containing simulated data for baseline model </span></li> <li> <p><span>sim_data_interactions_pos.tar.gz: directory containing simulated data for interactions model with positive interaction effects </span></p> </li> <li> <p><span>sim_data_interactions_neg.tar.gz: directory containing simulated data for interactions model with negative interaction effects </span></p> </li> <li><span>NMU.xlsx: spreadsheet containing data from the <em>NMU</em> RT-qPCR experiment </span></li> </ul>
Human pancreatic cancer single cell atlas reveals association of CXCL10+ fibroblasts and basal subtype tumor cells
Open the record for dataset details and reuse information.
Comparison of Fixed Single Cell RNA-seq Methods to Enable Transcriptome Profiling of Neutrophils in Clinical Samples - Time course data
<p>Monitoring neutrophil gene expression is a powerful tool for understanding disease mechanisms, developing new diagnostics, therapies and optimizing clinical trials. Neutrophils are sensitive to the processing, storage and transportation steps that are involved in clinical sample analysis. This study is the first to evaluate the capabilities of technologies from 10X Genomics, PARSE Biosciences, and HIVE (Honeycomb Biotechnologies) to generate high-quality RNA data from human blood-derived neutrophils. Our comparative analysis shows that all methods produced high quality data, importantly capturing the transcriptomes of neutrophils. 10X FLEX cell populations in particular showed a close concordance with the flow cytometry data. Here, we establish a reliable single-cell RNA sequencing workflow for neutrophils in clinical trials: we offer guidelines on sample collection to preserve RNA quality and demonstrate how each method performs in capturing sensitive cell populations in clinical practice.</p> <p><strong>This dataset includes only the 10X Flex time course data and analysis.</strong></p>
Single-cell datasets for Spherical Manifolds Capture Drug-Induced Changes in Tumor Cell Cycle Behavior
<p>Single-cell dataset for Spherical Manifolds Capture Drug-Induced Changes in Tumor Cell Cycle Behavior by Wen et al. This is a single-cell T47D ER+/HER2- cancer dataset, where rows are individual cells, and columns are proteomic features measured using iterative immunofluorescent imaging (4i). Cell cycle phase annotations are found in the 'phase' column, and the 'Metadata_well' column refers to nanomolar treatment doses of palbociclib, from an untreated population (0 nM), up to 1,000 nM. Data are z-normalized across all treatment conditions. Please refer to the manuscript for full experimental details.</p>
Dataset: Light-regulated chloroplast morphodynamics in a single-celled dinoflagellate
<p>This repository contains the files for Figures 1-4 of the manuscript and SI figures 2-4. Every folder contains a readme file with further description. Folders contain analyzed and raw microscopy data. </p>
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.