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SRX9341674: GSM4848109: Unwounded Dorsal Skin scRNA-seq; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 30.3M spots, 2.5G bases, 1,005.6Mb downloads

Submitted by: NCBI (GEO)
Study: Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration [scRNA-seq]
show Abstracthide Abstract
Tissue regeneration is a process that recapitulates the molecular and mechanical aspects of development and evolution. We use the wound-induced hair neogenesis (WIHN) model to investigate the mechanical and molecular responses of the laboratory (Mus) and African spiny (Acomys) mice. Laboratory and spiny mice showed an opposite trend of spatiotemporal morphogenetic field for WIHN during wound healing, and wound stiffness gradient across the whole wound bed predicated pattern of hair formation. Using bulk and single-cell RNA-seq analysis and K14-Cre-Twist1 transgenic mice, we identified the central role of the Twist1 pathway as the mediator of epidermal-dermal interaction and the emergence of periodic hair primordia. Lastly, we generated a Turing model with an underlying measure of stiffness to support a two-scale tissue mechanic model to explain the setup of a morphogenetic field from a wound bed (mm scale) or periodically arranged hair primordia from a morphogenetic field (µm scale). Delineating the common and distinct chemo-mechanical events during regenerative wound healing between laboratory and African spiny mice reveal its evo-devo advantages, which provide new perspectives for regenerative medicine. Overall design: Single-cell mRNA sequencing for back skin from naïve mice using Drop-Seq
Sample: Unwounded Dorsal Skin scRNA-seq
SAMN16516536 • SRS7572359 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Single cells were isolated from excised tissue from naïve animals (pooled from 3 wounds) using a collagenase/dispase digestion. Cells were stained with antibodies against CD45 (hematopoietic), CD31 (endothelial) and Ter119 (red blood cells); live cells were discriminated with DAPI. At least 100,000 live, CD45-CD31-Ter119- cells were subjected to single cell capture and droplet formation following instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper. In brief, cells at 150,000 cells/ml, barcoded beads at 175,000 beads/ml and droplet generation oil were co-flowed at a rate of 4, 4, and 15 ml/hour, respectively, in a PDMS microfluidics chip to generate oil droplets containing beads and lysed cells. Post flow, droplets were broken and reverse transcription performed. Complementary DNA was PCR amplified, magnetically cleaned up and subjected to tagmentation and sequencing library construction. Prepared libraries were cleaned up and sequenced via Illumina HiSeq4000 or NovaSeq. Drop-seq protocol v.3.1; uses Illumina reagents
Experiment attributes:
GEO Accession: GSM4848109
Links:
Runs: 1 run, 30.3M spots, 2.5G bases, 1,005.6Mb
Run# of Spots# of BasesSizePublished
SRR1287565030,276,7022.5G1,005.6Mb2023-10-24

ID:
12196061

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