Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An Integrated Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit

ABSTRACT: Single-cell and spatial transcriptomics have transformed our ability to chart human tissue organization at unprecedented resolution. These technologies enable the construction of high-quality reference atlases, essential for mapping healthy tissue architecture and identifying robust gene markers. We developed a healthy Human Skin Cell Atlas (HSCA), systematically integrating 34 public datasets and totaling 819,068 cells, with curated metadata and harmonized cell type nomenclature to ensure consistency. We place particular emphasis on the pilosebaceous unit, a key epithelial structure critical for both homeostasis and pathology. While prior studies captured the interfollicular epidermis and immune landscape in detail, deeper hair follicle regions remained under-characterized. By leveraging high-resolution spatial transcriptomics (Visium HD), we spatially resolved and transcriptionally defined the lower hair follicle compartments and pinpointed important signalling hubs. Furthermore, the HSCA enables the detection of cell types not detectable in standalone datasets, such as Merkel cells. Our results illustrate the value of the integrated single-cell atlas and spatial data in refining tissue organization and highlight the PSU as a complex and diverse epithelial niche.

ORGANISM(S): Homo sapiens

PROVIDER: GSE308929 | GEO | 2026/06/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma - Spatial Transcriptomics - 10X Visium

Project description:Our understanding of how human skin cells differ according to anatomical site and tumour formation is limited. To address this we have created a multi-scale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single cell RNA sequencing, spatial global transcriptional profiling and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retained signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling. We propose that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community.

2023-12-22 | E-MTAB-13085 | biostudies-arrayexpress

Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma - Spatial Transcriptomics - 10X Visium

Project description:Our understanding of how human skin cells differ according to body site and tumour formation is limited. To address this we have created a multi-scale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single cell RNA sequencing, spatial global transcriptional profiling and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retain signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling during cancer neovascularization. Our findings suggest that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community.

2023-12-22 | E-MTAB-13084 | biostudies-arrayexpress

Transcription profiling of Gata3 conditional knock out mice to investigate epidermis and hair follicle differentiation

Project description:Transcriptome analysis on Gata3 conditional knock out murine hair follicles. Background. The transcription factor Gata3 is critically involved in epidermis and hair follicle differentiation. Yet, little is known about how Gata3 co-ordinates stem cell lineage determination in skin, which processes are mostly implicated and how Gata3 differentially regulates distinct cell populations within the hair follicle. Here, we describe a conditional Gata3-/- mouse (K14-Gata3-/-) in which Gata3 is specifically deleted in epidermis and hair follicles. Principal findings. K14-Gata3-/- mice show aberrant postnatal growth and development, delayed hair growth and maintenance, abnormal hair follicle organization and irregular pigmentation. After the first hair cycle, the germinative layer surrounding the dermal papilla was not restored; instead, proliferation was pronounced in basal epidermal cells. Transcriptome analysis of laser-dissected K14-Gata3-/- hair follicles as compared to wild type littermate controls, revealed mitosis, epithelial differentiation and the Notch, WNT and BMP signalling pathways to comprise significantly overrepresented processes. Conclusions. Subsequent elucidation of these pathways at the RNA and protein levels and physiologic endpoints shows that Gata3 integrates diverse signalling networks to regulate the balance between hair follicle and epidermal cell fates.

2007-01-01 | E-MEXP-634 | biostudies-arrayexpress

Spatially resolved proteomic mapping in skin organoid for hair follicle development

Project description:Hair follicle development is a complex, highly regulated process involving interactions between epithelial and mesenchymal cells. However, the specific molecular mechanisms and important biological processes of hair follicle development remain poorly understood. In this study, we applied spatially resolved proteomic mapping to investigate the process of hair follicle development in skin organoids at different stages: D55, D75, D90, D140, D150, and D170, which corresponds to that from hair germ formation to hair follicle aging. Our analysis identified dynamic changes in protein expression and active protein synthesis during hair follicle appearance. The results provide a comprehensive spatial proteomic map of hair follicle development and offer new insights into the biological process driving hair follicle formation and maturation. These findings may guide future therapeutic strategies for hair regeneration and the treatment of hair disorders.

2025-04-08 | PXD062716 |

The citrullinating enzyme PADI4 governs progenitor cell proliferation and translation in developing hair follicles

Project description:Posttranslational protein modifications have emerged as a mechanism regulating progenitor cell state transitions during tissue formation. Herein, we exploit the stereotyped hair follicle development to delineate the function of PADI4; an enzyme converting peptidylarginine to citrulline. Single cell-sequencing places Padi4 in both progenitor and differentiated hair lineage cells and indicate that PADI4 acts to repress transcription during hair follicle development. We establish PADI4 as a negative regulator of proliferation, acting on LEF1-positive hair shaft committed progenitor cells. Mechanistically, PADI4 citrullinates proteins associated with mRNA-processing and ribosomal biogenesis, and lack of PADI4 promotes protein synthesis and rRNA transcription in vivo. Characterizing key translational effectors, we demonstrate that PADI4 citrullinates the translational repressor 4E-BP1 and reveal a crosstalk between PADI4 activity and 4E-BP1 phosphorylation. This work sheds new light on how posttranslational modifications impact progenitor cell states and tissue formation.

2025-07-28 | PXD064137 | Pride

Sphingolipid metabolism orchestrates the establishment of the adult hair follicle stem cell niche to control skin homeostasis

Project description:Bioactive sphingolipids serve as an essential building block of membranes, forming a selective barrier ensuring subcellular compartmentalization and facilitating cell type-specific intercellular communication through regulation of the plasma membrane receptor repertoire. How the cell type-specific lipid compositions are achieved and what is their functional significance in tissue morphogenesis and maintenance has remained unclear. Here, we identify a stem-cell specific role for ceramide synthase 4 (CerS4) in orchestrating fate decisions in the skin epidermis. Deletion of CerS4 in the epidermis prevents the effective establishment of the adult hair follicle bulge stem cell (HFSCs) niche due to altered differentiation trajectories of HFSC precursors towards upper hair follicle and inner bulge fates. Mechanistically, the HFSC differentiation defects arise from a stem cell intrinsic imbalance of key ceramides and sphingolipids, and associated hyperactivity of canonical Wnt signaling. The lack of HFSCs leads to disruption of hair follicle architecture and hair follicle barrier function, ultimately triggering a Th2-dominated immune infiltration closely resembling human atopic dermatitis. This work uncovers a fundamental role for a cell state-specific sphingolipid profile in epidermal stem cell homeostasis and the role of an intact stem cell niche in maintaining an intact skin barrier.

2025-01-23 | PXD047573 | Pride

Spatial transcriptomics of autoimmune alopecia

Project description:Autoimmune alopecia is a prevalent, highly morbid disease. The inflammatory pathways causing hair loss are not well characterized. We profiled two tissue microarrays comparing healthy skin to scarring alopecia and alopecia areata via spatial transcriptomics to analyze the genes and pathways dysregulated in autoimmune alopecia in direct proximity to the hair follicle.

2023-09-25 | GSE227632 | GEO

Single-Cell Transcriptomics Reveals the Differentiation and Spatial Signatures underlying Sheep Hair Follicle Heterogeneity and Wool Curvature

Project description:Here, Single-cell suspensions from the wavy wool and straight wool lambskins were prepared for unbiased single-cell RNA sequencing (scRNA-seq). Based on UAMP analysis, we identified 19 distinct populations from 15,830 single-cell transcriptomes and delineated their cellular identity from specific gene expression profiles. Furtherly, novel marker gene was applied in identifying dermal papilla cells isolated in vitro. By using pseudotime ordering analysis, we successfully constructed the epithelium cell lineage differentiation trajectory and revealed the dynamic gene expression profiles of matrix progenitors’ commitment to the hair shaft and inner root sheath (IRS) cells. Meanwhile, intercellular communication between different cell populations was inferred based on CellChat and the priori knowledge of ligand-receptor pairs, as a result strong intercellular communication and associated signaling pathways were revealed. Besides, to clarify the molecular mechanism of wool curvature, differentially expressed genes in specific cells between straight wool and curly wool were identified and analyzed. Our findings here provide unbiased and systematic view of transcriptional organization of sheep hair follicle, reveal the differentiation and spatial signatures underlying sheep hair follicle heterogeneity and wool curvature, which will provide a valuable resource for understanding the molecular pathways involved in sheep hair follicle development.

2022-01-12 | GSE186204 | GEO

Dynamic chromatin architecture in ovarian follicle development in chickens

Project description:Ovarian follicle development is a complex and well orchestrated biological process. Chromatin spatial organization has emerged as an important regulator of gene expression, but how these changes during follicle development are still unknown. Here, we integrated RNA-seq analyses of chicken follicular granulosa cells of 10 developmental stages. Our data revealed that SWF, F1, and POF had the greatest transcriptome differences from other stages. Our results provide a genome-wide atlas of chromatin interactions during chicken ovarian follicle development.

2023-04-19 | GSE229714 | GEO

Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

Project description:Ovarian follicle development is a complex and well orchestrated biological process. Chromatin spatial organization has emerged as an important regulator of gene expression, but how these changes during follicle development are still unknown. Here, we integrated RNA-seq and Hi-C analyses of chicken follicular granulosa cells of 10 developmental stages. Our data revealed that SWF, F1, and POF had the greatest transcriptome differences from other stages. Our results provide a genome-wide atlas of chromatin interactions during chicken ovarian follicle development.

2021-11-10 | GSE167064 | 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