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6,040
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6,040 results for “Single-Cell”
Automatic monitoring of neural activity with single-cell resolution in behaving Hydra
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Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection
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A single-cell atlas of circulating immune cells over the first two months of age in extremely premature infants
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Seurat objects for the manuscript Single-cell consequences of X-linked meiotic drive in stalk-eyed flies
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Anabaena circadian clock behavior under nitrogen-poor conditions from single-cell measurements of fluorescence intensity
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Single-cell RNA sequencing of the testis of drive and standard Teleopsis dalmanni males
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Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 3)
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Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 1)
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Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 4)
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Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 2)
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Generating an expression matrix for droplet single-cell RNA-seq (dscRNA-seq) data
<p>This tutorial is adapted from the 'Generating an expression matrix' training session at the EBI (https://www.ebi.ac.uk/training/events/2019/single-cell-rna-seq-analysis-questions-clusters).</p>
SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections (Revision data)
<p>The submitted dataset, correspond to the RAW (*.czi format) and analysis files of the <strong>revisions</strong> of manuscript "SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections", which has been processed for revision (2020-01-31) by PLOS Biology.</p> <p>The files are in *.zip format and the naming follows thenumbering of the manuscript figures, which will be found in bioRxiv.org (<strong>ID#: BIORXIV/2020/938571</strong>). Each *.zip files contains a document with the description of all the provided files.</p>
Global Characterization of Megakaryocytes in Bone Marrow, Peripheral Blood, and Cord Blood by Single-cell RNA Sequencing
<p><span><span>Megakaryocytes (MK) are mainly derived from bone marrow (BM) and are mainly involved in platelet production. Recent studies have shown that MK derived from BM may have immune function, and that MK from peripheral blood (PB) are associated with prostate cancer. We analyzed more than 1.2 million single-cell transcriptome data from 132 samples of PB, BM, and cord blood (CB) from healthy individuals and patients, and obtained 4474 MK single cell and 14 MK subtypes. We found that MK were widely distributed and the amount of MK in PB was more than that in BM and there were specificity MK subtypes in PB. We found classical MK1 with typical MK characteristics and non-classical MK2 closely related to immunity which was the most common subtype in BM and CB. Classical MK1 was closely related to Non-Small Cell Lung Cancer (NSCLC) and has diagnostic ability. MK2 may have potential adaptive immune function and play a role in tumor NSCLC and autoimmune diseases Systemic Lupus Erythematosus. This study deepened our understanding of MK and suggested that MK had potential immune functions and was involved in various diseases.</span></span></p>
Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS
<p>Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS. Gene expression and immune receptor repertoire sequencing was performing for both B and T cells. This dataset contains the VDJ sequencing information for the four samples. Each B cell and T cell library was sequenced across four lanes. </p> <p> </p> <p>Files with _WT_ in their name correspond to the young (4-6 week B6 mice) </p> <p>Files with _12_ in their name before the BDJ or VDJ text correspond to the 12-month-old cohort.</p> <p>Files with _18_ in their name before the BDJ or VDJ text correspond to the 18-month-old cohort in which four brains were pooled.</p> <p>Files with 4_18_ in their name before the BDJ or VDJ text correspond to the 18-month-old mouse that was processed and sequenced alone. </p> <p> </p> <p>The L001 - L004 in the file names indicates the sequencing lane. Samples with BDJ correspond to the B cell repertoire library (B cell VDJ). Samples with TDJ correspond to the T cell repertoire library (T cell VDJ). </p>
Single-cell immune repertoire sequencing of two convalescent COVID-19 patients
<p>Single-cell immune repertoire sequencing of two convalescent COVID-19 patients using 10x genomics 5' immune profiling. Resulting output files are from the count and vdj functions from 10x genomic's cellranger v3.1.0. </p>
AnnData files for "Human dermal fibroblast subpopulations are conserved across single-cell RNA sequencing studies"
<p>AnnData files for "Human dermal fibroblast subpopulations are conserved across single-cell RNA sequencing studies". </p> <p>Includes Joined dataset with all four datasets at once.</p>
Prioritization of cell types responsive to biological perturbations in single-cell data with Augur
<p>Processed and analysis-ready input data discussed in our Augur procedures.</p>
Data of quantitative, ratiometric dual fluorescence reporter assay at the single-cell level
<p>The data set shows the evaluation of a new dual fluorescence reporter assay using three test genes, vimentin, lamin A/C and Arp3. This fluorescence protein-based reported assay successfully predicts siRNA efficacy with high fidelity. Data include images of Hela cells transfected with Vim-T4 ad Vim-T5 knockdown contructs; images of dual fluorescence assay; data analysis for knockdown experiments, Western blotting analysis of vimentin-knockdown in Hela cells, knockdown of endogenous lamin A/C in Hela cells; quantification of lamin A/C knockdown in Hela cells; dual fluorescence assay of human vimentin genes using three plasmids; Western blotting of Arp3 knockdown in SCC9 cells.</p> <p>All files can be opened using LibreOffice or OpenOffice. Some of the ODS files have a minor problem when opening them in Excel in the Windows computers. Excel will give warning about some unreadable contents. By choosing the repair option, the file contents will be shown without changes compared to the original data. Detailed explanation is given in the “Explanation file”.</p>
Single-cell ATAC-seq control of cross-contaminations (experiment 2)
<p>On the Fluidigm C1 platform for single-cell analysis, the cells are captured in 96 chambers arranged serially, and then washed before further processing. Thus, debris present from the loading medium or released by captured cells upstream are a possible source of contamination. We generated a control datasets using the single-cell ATAC-seq protocol available from Fluidigm's ScriptHub. We cultivated human Hep G2 and mouse Hepa 1-6 (both are liver cancer cell lines), stained them with green and red calceins (respectively), and loaded them at equal concentration in a Fluidigm medium flow cell (old design), before running the C1 single-cell ATAC-seq program. To evaluate damage and carry-over of debris from FACS-sorting, two IFCs were run in two C1 machines in parallel. In the first (flowcell ID 1772-123-155), the cells not washed and in the second, they were washed (ID 1772-123-158).</p> <p>The data deposited here is a sequencing run (Illumina MiSeq) of these ATAC-seq libraries. The metadata indicating the contents of each well is being uploaded separately and this record will be updated once the DOIs are available.</p>
Single-cell ATAC-seq control of cross-contaminations (experiment 1)
<p>On the Fluidigm C1 platform for single-cell analysis, the cells are captured in 96 chambers arranged serially, and then washed before further processing. Thus, debris present from the loading medium or released by captured cells upstream are a possible source of contamination. We generated a control datasets using the single-cell ATAC-seq protocol available from Fluidigm's ScriptHub. We cultivated human Hep G2 and mouse Hepa 1-6 (both are liver cancer cell lines), stained them with green and red calceins (respectively), and loaded them at equal concentration in a Fluidigm medium flow cell (old design), before running the C1 single-cell ATAC-seq program.</p> <p>The data deposited here is a sequencing run (Illumina MiSeq) of these ATAC-seq libraries. The metadata indicating the contents of each well is being uploaded separately and this record will be updated once the DOIs are available.</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.