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Single cell RNA sequencing analysis of mouse skin samples with multiple conditions (10x scRNA-seq)

ABSTRACT: Single cell RNA sequencing analysis of mouse skin samples with multiple conditions (10x scRNA-seq)

PROVIDER: PRJNA815629 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18311600.fastq.gz	Fastqsanger.gz
	SRR18311601.fastq.gz	Fastqsanger.gz
	SRR18311602.fastq.gz	Fastqsanger.gz
	SRR18311603.fastq.gz	Fastqsanger.gz
	SRR18311604.fastq.gz	Fastqsanger.gz

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Single cell RNA sequencing analysis of mouse skin samples with multiple conditions (10x scRNA-seq)

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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)

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