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80 results for “single-cell ATAC-seq”
Training material for the mapping and quantification of single-cell ATAC-seq 10X Datasets
<p>The data provided here is part of the Galaxy Training Network tutorial that analyses 10x genomics single-cell ATAC-seq data from the 10x platform. The original data is from 1k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor.</p> <p>Due to time constraints during training, the datasets were subsampled to reads that map to chromosome 21 only.</p> <p>The 10x Genomics Datasets follow the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution</a> license.</p> <p>There is an additional count matrix in Anndata format created from full datasets.</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>
Single cell ATAC-seq Mouse Kidney Data: Chromatin-accessibility estimation from single-cell ATAC data with scOpen
<p>We provide results regarding the bioinformatic analysis of scATAC-seq from mouse UUO kidney at different time points.</p>
Training material for the mapping and quantification of single-cell ATAC-seq 10X Datasets
<p>The data provided here is part of the Galaxy Training Network tutorial that analyses 10x genomics single-cell ATAC-seq data from the 10x platform. </p> <p>Due to time constraints during training, the datasets were subsampled to reads that map to chrY.</p> <p>The 10x Genomics Datasets follow the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution</a> license.</p>
CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal - Appendix
Open the record for dataset details and reuse information.
Single-cell ATAC-seq analysis of human plasma cell differentiation
GEO Series GSE242324. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis [ATAC-seq]
GEO Series GSE133785. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell combinatorial indexing ATAC-seq of HCC1143 with MEK, PI3K, and BET inhibition
GEO Series GSE126261. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Single-cell ATAC-Seq of cells recruited to regenerative portions of large skin wounds.
GEO Series GSE131600. Mus musculus. 1 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A feedback amplifier circuit with Notch and E2A orchestrates T-cell fate and suppresses the innate lymphoid cell lineages during thymic ontogeny [Single-cell RNA + ATAC-Seq]
GEO Series GSE254290. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation [bulk ATAC-Seq]
GEO Series GSE96771. Homo sapiens. 13 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell ATAC-seq of mouse thymus iNKT cells
GEO Series GSE141825. Mus musculus. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell ATAC-seq analysis of hESCs undergoing neuronal differentiation exposed to paracetamol [scATAC-seq]
GEO Series GSE220026. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Integrative Single-Cell RNA-Seq and ATAC-Seq Identifies Transcriptional and Epigenetic Blueprint Guiding Osteoclastogenic Trajectory [scATAC-seq]
GEO Series GSE288654. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell ATAC-seq analysis of mouse embryonic stem cells before and after Cohesin depletion
GEO Series GSE266089. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Human single cell ATAC-seq blood)
GEO Series GSE123895. Homo sapiens. 480 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell ATAC-Seq of Adult GBM surgical specimens
GEO Series GSE139136. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Ets1 ATAC-Seq]
GEO Series GSE239801. Mus musculus. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell ATAC-seq of developing cortical interneurons.
GEO Series GSE165031. Mus musculus. 13 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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
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DANDI Archive for NWB datasets
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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.