Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA542149: Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming

Source: NCBI / GSE130973
Submission Date: May 09 2019
Release Date: Mar 31 2020
Update Date: May 07 2020

Summary: Fibroblasts are the main dermal cell type and are essential for the architecture and function of human skin. Important differences have been described between fibroblasts localized in distinct dermal layers, and these cells are also known to perform varied functions. However, this phenomenon has not been analyzed comprehensively yet. Here we have used single-cell RNA sequencing to analyze >15,000 cells from a sun-protected area in young and old donors. Our results define four main fibroblast subpopulations that can be spatially localized and functionally distinguished. Importantly, intrinsic aging reduces this fibroblast ‘priming’, generates distinct expression patterns of skin aging-associated genes, and substantially reduces the interactions of dermal fibroblasts with other skin cell types. Our work thus provides comprehensive evidence for a functional specialization of human dermal fibroblasts and suggests that the age-related loss of fibroblast priming contributes to human skin aging.

Overall Design: Overall 5 samples were analyzed. Two of them are from young subjects (age=25) and serve as replicates, three of them are from old subjects (age >= 50) and serve as replicates.

GEN Datasets:
GEND000117
Strategy:
Species:
Tissue:
Healthy Condition:
Development Stage:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: For each experiment, 4-mm punch biopsies were obtained from healthy whole skin specimens, immediately after resection from the inguinoiliac region of five male subjects. Samples were kept in MACS Tissue Storage Solution (Miltenyi Biotec) for no longer than 1 h before their enzymatical and mechanical dissociation with the Whole Skin Dissociation kit for human material (Miltenyi Biotec) and the Gentle MACS dissociator (Miltenyi Biotec), following the manufacturer's instructions. Cell suspensions were then filtered through 70-μm cell strainers (Falcon) and depleted of apoptotic and dead cells with the Dead Cell Removal Kit (Miltenyi Biotec).
Library Construction Protocol: Sequencing libraries were subsequently prepared following the Drop-seq methodology (Macosko et al., 2015), using a Chromium Single Cell Controller and the v2 chemistry from 10X Genomics. Thus, approximately 20,000 cells per sample were mixed with the retrotranscription reagents and pipetted into a Chip A Single Cell, also containing the Single Cell 3‘ Gel Bead suspension and Partitioning Oil. The Chip was subsequently loaded into a Chromium Single Cell Controller (10X Genomics) where the cells were captured in nanoscale droplets containing both the reagents needed for reverse transcription and a gel bead. Resulting Gel Bead-In-EMulsions (GEMs) were then transferred to a thermocycler in order to perform the retrotranscription following the manufacturer’s protocol. Each gel bead contained a specific 10X Genomics barcode, an Illumina R1 sequence, a Unique Molecular Identifier (UMI) and a poly-dT primer sequence. Therefore, from poly-adenylated mRNA the reaction produced full-length cDNA with a unique barcode per cell and transcript, which allowed tracing back all cDNA coming from each individual cell. Following an amplification step, cDNA was further processed by fragmentation, end repair and A-tailing double-sided size selection using AMPure XP beads. Finally, Illumina adaptors and a sample index were added through PCR using a total number of cycles adjusted to the cDNA concentration. After sample indexing, libraries were again subjected to double-sided size selection. Quantification of the libraries was carried out using the Qubit dsDNA HS Assay Kit (Life Technologies), and cDNA integrity was assessed using D1000 ScreenTapes (Agilent Technologies). Paired-end (26+74bp) sequencing (100 cycles) was finally performed with a HiSeq 4000 device (Illumina).
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina HiSeq X Ten
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming.
Communications biology . 2020-04-23 [PMID: 32327715]