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271 results for “scATAC”
scATAC data from: Organization of the human intestine at single cell resolution
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Processed scRNA and scATAC data in DRCTdb
<p><span>Understanding the molecular mechanisms underlying </span><span>genetic</span><span> diseases is challenging due to the involvement of both environmental and genetic factors. Genome-wide association studies (GWAS) have identified numerous genetic loci, but their functional implications remain largely unknown. Single-cell multiomics sequencing has emerged as a powerful tool to study disease-specific cell types and their relationship with genetic variants. However, there is a lack of comprehensive databases for exploring genetic disease-related cell types and their mechanisms across different human tissues. In this study, we present the disease-related cell type database (DRCTdb), a database that integrates GWAS data and single-cell multiomics data to identify disease-related cell types and elucidate their regulatory mechanisms. DRCTdb contains well-processed single-cell multiomics data in 16 studies, encompassing transcriptome and epigenetic information overall 4 million cells within 28 tissues. Through DRCTdb, user can easily browse relationships and regulatory mechanisms between SNPs of 42 genetic disease and cell type in different human tissue based on GWAS and single cell multiomics data. Moreover, DRCTdb also provides data download,</span><span> which</span><span> allowing users to download well-processed <a name="_Int_HEP27DcN"></a>single-cell multiomics data and analysis result from DRCTdb</span></p>
scNCL transfers labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization
<p>Data used in our manuscript.</p> <p>'scNCL_data' folder contains gene expression data (with protein) and gene activitiy data (with protein).</p> <p>'GLUE_data' folder contains gene expression data and raw chromatin accessibility data. </p> <p>'HFA-resampling' folder contains multiple independent sampling of HFA-subset dataset.</p> <p>'Accuray on HFA-subsets.xlsx' file contains accuray results of all compared methods on HFA-subsets datasets.</p>
Reference datasets of SCRIP for scATAC-seq
<p>Transcription regulators and histone modifications reference for SCRIP</p> <p>SCRIP can be downloaded from <a href="http://github.com/wanglabtongji/SCRIP">https://github.com/wanglabtongji/SCRIP</a></p> <p>Curated annotation from Cistrome Data Browser</p> <p>Version: 0.0.220112</p> <p>Release date: 2022-01-12</p>
Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scATAC-seq]
GEO Series GSE191282. Homo sapiens. 1 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids [scATAC-seq]
GEO Series GSE252523. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [scATAC-seq]
GEO Series GSE192738. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Divergent clonal differentiation trajectories of T cell exhaustion (scATAC-seq)
GEO Series GSE188669. Mus musculus. 11 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients [scATAC-seq]
GEO Series GSE242085. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
An atlas of gene regulatory networks for T memory cells in youth and old age [scATAC-seq]
GEO Series GSE228660. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
scATAC-seq of OT-1 CD8+ T cells from different time-course of Lm-OVA infected mice
GEO Series GSE241714. Mus musculus. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-cell analysis of accessible chromatin in human mammary epithelial cells using scATAC-seq [scATAC-seq]
GEO Series GSE135412. Homo sapiens. 288 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
CREBBP/EP300 acetyltransferase inhibition targets lineage specific enhancers to inhibit the proliferation of ER+ breast cancer cells [scATAC-Seq]
GEO Series GSE190162. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide maps of chromatin state in cultured male germline stem cells with retinoic acid treatment [scATAC-seq]
GEO Series GSE167531. Mus musculus. 1 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
single-cell chromatin accessibility profiling of mouse gonads during sex determination [scATAC-seq]
GEO Series GSE218995. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [PBMC scATAC]
GEO Series GSE216903. Homo sapiens. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Maternal IL-10 restricts fetal emergency myelopoiesis [scATAC-seq]
GEO Series GSE240914. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Differential usage of Zeb2 enhancer distinguishes adult and embryonic hematopoiesis [scATAC-seq]
GEO Series GSE167329. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CC100_scATAC]
GEO Series GSE115216. Homo sapiens. 192 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A CRISPR-Activation CROP-seq Screen Identifies HMGN1 as a Dosage Sensitive Regulator of Heart Defects in Down Syndrome (scATAC-Seq)
GEO Series GSE271445. Homo sapiens. 4 samples. Type: Genome binding/occupancy 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.