A major goal of the Skin Biology and Diseases Resource Center (SBDRC) at Mount Sinai is to provide high-end genomics, transcriptomics, and imaging services that are specifically tailored to research in skin biology and diseases to accelerate progress and innovation. Constant advancement in such multiomic approaches enables scientists to launch hypothesis-driven projects that were inconceivable in the near past. To complete such multidisciplinary projects, strong skin-biology domain knowledge (i.e. deep understanding of skin development, regeneration, and pathologies) must be coupled with solid statistical and study design support, as well as innovative bioinformatic and integrative data analysis solutions.
The mission of the Center’s Data Analysis and Integration Core D is to support the planning, analysis, integration, and interpretation of all multiomics and imaging data generated by the SBDRC services. Specifically, Core D focuses on: (i) integrating data to generate meaningful insights and propose follow-up mechanistic experiments; (ii) ensuring data reproducibility and scientific rigor; (iii) developing innovative web-based tools to allow integrative and user-friendly data sharing; and (iv) providing learning opportunities to promote the next-generation of skin biologists who will be able to close the gap between wet-lab and dry-lab scientists (i.e. skin biologists who are also biostatisticians, bioinformaticians, and epidemiologists).
Our Web Tools
Skin-GLOW (Skin-Gene Level Omic Web Tool) is a user-friendly, interactive, web-based visualization tool that allows users to compare expression levels of a specific gene across multiple mouse-skin-related datasets. These datasets were curated from published studies that performed bulk RNA-sequencing of FACS-isolated cell types of embryonic, neonatal, and postnatal mouse skin. Data were further evaluated for their quality, and processed to generate normalized gene expression counts to allow comparisons across samples. Skin-GLOW further allows users to choose the type of data to visualize, specify the way data should be displayed (e.g., plot type), and download high-resolution images for presentations and publications. Links to manuscripts on PubMed and data on GEO are also available. Skin-GLOW is available to all SBDRC users and the broader skin scientific community. Skin-GLOW is developed and maintained by Core D personnel.
Skin-EpiGlow (Skin-Epigenetics Gene Level Omic Web Tool) is a user-friendly, interactive, web-based visualization tool that allows users to visualize patterns of chromatin accessibility and enrichment of various histone post translational modifications at promoters and associated enhancers of specific genes, across multiple mouse-skin-related datasets. These datasets were curated from published studies that performed bulk ATAC-sequencing and ChIP-sequencing of FACS-isolated cell types of embryonic, neonatal, and postnatal mouse skin. Data were further evaluated for their quality, and processed to generate normalized counts to allow comparisons across samples. Skin-EpiGLOW provide users access to an interactive session on the UCSC Genome Browser to visualize enrichment levels. Links to manuscripts on PubMed and data on GEO are also available. Skin-EpiGLOW is available to all SBDRC users and the broader skin scientific community. Skin-EpiGLOW is developed and maintained by Core D personnel.
HMS Browser (Human-Mouse Skin Browser) allows researchers to utilize curated single-cell RNA-seq data to explore cell-type-specific gene expression patterns. The tool further enables human-mouse cross-species comparisons of cell-type-specific gene expression, with cell-type annotations for cells from the interfollicular epidermis, pilosebaceous unit, and mesenchymal compartments. This dataset was curated from multiple studies, evaluated for its quality, and integrated to allow comparisons across samples. HMS Browser further allows users to visualize gene expression and cell-type annotations using dimensionality reduction methods such as 2D and 3D interactive UMAPs as well as violin plots across cell types, donors, and datasets in both organisms. Links to manuscripts on PubMed and data on GEO are also available. HMS Browser is available to all SBDRC users and the broader skin scientific community.
HMS Browser Citation: Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells. Thrane K, Winge MCG, Wang H, Chen L, Guo MG, Andersson A, Abalo XM, Yang X, Kim DS, Longo SK, Soong BY, Meyers JM, Reynolds DL, McGeever A, Demircioglu D, Hasson D, Mirzazadeh R, Rubin AJ, Bae GH, Karkanias J, Rieger K, Lundeberg J, Ji AL. J Invest Dermatol. 2023 May 2:S0022-202X(23)02040-7. doi: 10.1016/j.jid.2023.02.040. Online ahead of print. PMID: 37142187
For any questions regarding the web tools please contact: dan.hasson@mssm.edu or deniz.demircioglu@mssm.edu.