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Epidermal basal domains organization highlights skin robustness to environmental exposure [scRNA-seq]

ABSTRACT: Epidermal basal domains organization highlights skin robustness to environmental exposure [scRNA-seq]

PROVIDER: PRJNA847425 | ENA |

REPOSITORIES: ENA

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Epidermal basal domains organization highlights skin robustness to environmental exposure.

Project description:Epidermal basal domains organization highlights skin robustness to environmental exposure.

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Epidermal basal domains organization highlights skin robustness to environmental exposure [bulk RNA-seq]

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Binary organization of epidermal basal domains highlights robustness to environmental exposure

Project description:Adult interfollicular epidermis (IFE) renewal is likely orchestrated by physiological demands of its complex tissue architecture comprising spatial and cellular heterogeneity. Mouse tail and back skin display two kinds of basal IFE spatial domains that regenerate at different rates. Here, we elucidate the molecular and cellular states of basal IFE domains by marker expression and single-cell transcriptomics in mouse and human skin. We uncover two paths of basal cell differentiation that in part reflect the IFE spatial domain organization. We unravel previously unrecognized similarities between mouse tail IFE basal domains defined as scales and interscales versus human rete ridges and inter-ridges, respectively. Furthermore, our basal IFE transcriptomics and gene targeting in mice provide evidence supporting a physiological role of IFE domains in adaptation to differential UV exposure. We identify Sox6 as a novel UV-induced and interscale/inter-ridge preferred basal IFE-domain transcription factor, important for IFE proliferation and survival. The spatial, cellular, and molecular organization of IFE basal domains underscores skin adaptation to environmental exposure and its unusual robustness in adult homeostasis.

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Epidermal basal domains organization highlights skin robustness to environmental exposure [bulk RNA-seq]

Project description:Purpose: To unravel the molecular heterogeneity of distinct epidermal populations in interfollicular epidermis (IFE) in vivo Methods: We performed bulk RNA sequencing of FACS purified basal (Sca1+/alpha6-integrin+) IFE cells enriched in Slc1a3/Dlx1/Aspm CreER marked lineages. We used >10000 tdTomato+/Sca1+/α6-int+ (basal) cells from both back and tail skin at 2-weeks post TM induction from each of four CreER mouse lines and normalized them to Sca1+/α6-int+ sorted from the same mouse. Extracted RNA of high quality and low input was processed for library preparation followed by Illumina seq on HiSeq4000. The raw sample-specific FASTQ files were trimmed and mapped to the reference genome/transcriptome (mouse/mm10) and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression.

2022-07-05 | GSE205744 | GEO

Epidermal basal domains organization highlights skin robustness to environmental exposure.

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-07-05 | GSE205746 | GEO

Epidermal basal domains organization highlights skin robustness to environmental exposure [scRNA-seq]

Project description:Purpose: To unravel the molecular heterogeneity and characterise cell states of LRC/Non-LRC domains in interfollicular epidermis in vivo Methods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS purified basal (Sca1+/alpha6-integrin+) IFE cells as H2BGFP LRCs, mid-LRCs, and non-LRCs from K5-tTA x pTRE-H2BGFP mice. Single-cell suspension from back (2-week chase) and tail skin (3-week chase) was processed for the barcoded single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10x Genomics Cell Ranger pipeline (v3.1.0). The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate an expression matrix that was further analyzed in R using the Seurat package version 3.1. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained. Results: We obtained a total of 13484 and 14884 high quality cells from two different skin types after combining two datasets each from LRCs/mid-LRCs/Non-LRCs for further analysis by Seurat workflow Conclusions: Obtained high quality single cell transcriptomic data to dissect molecular and proliferative heterogeneity of interfollicular epidermis (IFE)

2022-07-05 | GSE205745 | GEO

Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network

Project description:Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network

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Transcriptional profiles of murine E13 epidermal cells and P4 epidermal basal cells

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