Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-Cell Chromatin Accessibility Landscape of Developing Perinatal Mouse Skin: A Multi-Omics Approach to Lineage Specification [scATAC-seq and scRNA-seq]

ABSTRACT: This study presents a time-series scATAC analysis of developing mouse skin. Motif and footprint analyses at the chromatin level, as well as integrated analysis with single-cell and spatial transcriptomic data, enable an in-depth identification of key transcription factors and driver genes involved in fibroblast differentiation and hair follicle formation. This study demonstrates the utility of scATAC analysis combined with multi-omics approaches in providing a comprehensive understanding of skin development. It serves as a valuable reference for future research on skin development and regeneration, supported by an interactive online portal.

ORGANISM(S): Mus musculus

PROVIDER: GSE286328 | GEO | 2026/03/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single-Cell Chromatin Accessibility Landscape of Developing Perinatal Mouse Skin: A Multi-Omics Approach to Lineage Specification

Project description:This study presents a time-series scATAC analysis of developing mouse skin. Motif and footprint analyses at the chromatin level, as well as integrated analysis with single-cell and spatial transcriptomic data, enable an in-depth identification of key transcription factors and driver genes involved in fibroblast differentiation and hair follicle formation. This study demonstrates the utility of scATAC analysis combined with multi-omics approaches in providing a comprehensive understanding of skin development. It serves as a valuable reference for future research on skin development and regeneration, supported by an interactive online portal.

2026-03-12 | GSE286129 | GEO

Patient-Derived Orthotopic Xenografts and Cell Lines from Pediatric High-Grade Glioma Recapitulate Heterogeneity of Histopathology, Molecular Signatures and Drug Response

Project description:We established 21 patient-derived pHGG orthotopic xenograft (PDOX) models and 8 matched cell lines from diverse pHGG subgroups. Models recapitulated histopathology, DNA methylation signatures, mutations and gene expression patterns of the patient tumors from which they were derived, and included rare subgroups not well-represented by existing models. We also included 6 DIPG cell lines generously shared by Dr. Michelle Monje (Stanford University). An online interactive data portal is available to explore associated detailed molecular characterization and HTS chemical sensitivity data.

2020-12-09 | GSE152035 | GEO

scATAC-seq of mouse Plasmodium-specific CD4+ T cells

Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 4, 7, and 32 to undergo processing and to generate scATAC-seq dataset. At Day 7, CXCR5+ and CXCR6+ cells were recovered separately. At Day 32, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.

2020-10-14 | E-MTAB-9402 | biostudies-arrayexpress

scATAC-seq of early brain organoid development from pluripotency

Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.

2022-08-18 | E-MTAB-11998 | biostudies-arrayexpress

Genome-wide maps of chromatin state in mouse perinatal testes [scATAC-seq]

Project description:We report the application of single-cell ATAC-seq to reconstruct the epigenetic program and identify key transcription factors and cis-regulatory elements during the perinatal testiscular develpment. First, we constructed sequencing libraries from testes collected from E18.5, PND0, PND3 and PND6 mice. The cell clusters identidied from scATAC-seq were assigned to known testicular cell types, including germ cells, Sertoli cells, Leydig cells, peritubular myoid cells, stromal cells, endothelial cells and blood cells. We then constructed pseudotime developmental trajectories and identified transcription factor regulators for each cell type. Lastly, we identified cis-regulatory elements such peak-to-gene linkages across testis.

2023-05-10 | GSE164439 | GEO

Designing a single cell ATAC-Seq (scATAC-Seq) dataset to benchmark scATAC-Seq analysis methods

Project description:Single cell sequencing technology has been widely used for understanding the heterogeneity of complex tissue and for identifying novel cell types or cell states. Previous efforts of single cell profiling are mostly performed by measuring transcriptomes using single cell RNA sequencing (scRNA-seq). scRNA-seq is relatively well developed and around 500 analysis tools are currently available for performing different tasks. In the past five years, assays for profiling the single cell chromatin accessibility landscape have emerged and provide extra information about gene regulation at the epigenetic level. Due to its simplicity and sensitivity, single cell Assays for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is widely used to obtain chromatin accessibility. This data will be used to comprehensively evaluate scATAC-seq data analysis tools and gaps in analysis workflows together with publicly available bulk ATAC-Seq and scATAC-seq data using optimised universal evaluation metrics.

2024-01-10 | GSE223319 | GEO

Single-cell chromatin accessibility data using scATAC-seq

Project description:Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.” Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.

2015-06-17 | E-GEOD-65360 | biostudies-arrayexpress

Single-Cell Chromatin Accessibility Landscape of Developing Perinatal Mouse Skin: A Multi-Omics Approach to Lineage Specification [scATAC-seq and scRNA-seq]

Project description:Single-Cell Chromatin Accessibility Landscape of Developing Perinatal Mouse Skin: A Multi-Omics Approach to Lineage Specification [scATAC-seq and scRNA-seq]

| PRJNA1208925 | ENA

Single cell profiling of a Caki-1:HeLa cell mixture by scATAC-seq and scGET-seq

Project description:A mixture of Caki-1 and HeLa cells in known proportions (80:20) is profiled using 10x Chromium scATAC-seq or scGET-seq protocols.

2021-08-17 | E-MTAB-9650 | biostudies-arrayexpress

Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells (scATAC-seq)

Project description:Understanding prostate response to castration and androgen receptor signaling inhibitors (ARSI) is critical to improving long-term prostate cancer (PCa) patient survival. Here we use a multi-omics approach on 229,794 single cells to create a mouse single-cell reference atlas better suited to interpreting mouse prostate biology and castration response. Our reference atlas refines single-cell annotations and provides chromatin context, which, when coupled with mouse lineage tracing demonstrates that the castration-resistant luminal cells are distinct from the pre-existent urethra-proximal stem/progenitor cells. Molecular pathway analysis and therapeutic studies further implicate JUN/FOS, WNT/b-Catenin, FOXQ1, NFkB, and JAK/STAT pathways as the major drivers of castration-resistant luminal populations with high relevance to human PCa. Importantly, we demonstrate the utility of our datasets, which can be explored through an interactive portal (https://visportal.roswellpark.org/data/tang/), to aid in developing novel combination treatments with ARSI for advanced PCa patients.

2024-06-14 | GSE227107 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data