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Series GSE189210 Query DataSets for GSE189210
Status Public on Nov 24, 2021
Title Parallel single cell multi-omics analysis of neonatal skin reveals transitional fibroblast states that restrict differentiation into distinct fates
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary One of the keys to achieving skin regeneration lies within understanding the heterogeneity of neonatal fibroblasts, which support skin regeneration. However, the molecular underpinnings regulating the cellular states and fates of these cells are not fully understood. To investigate this, we performed a parallel multi-omics analysis by processing neonatal murine skin for single-cell ATAC-sequencing (scATAC-seq) and single-cell RNA-sequencing (scRNA-seq) separately. Our approach revealed that fibroblast clusters could be sorted into papillary and reticular lineages based on transcriptome profiling, as previously published. However, scATAC-seq analysis of neonatal fibroblast lineage markers, such as, Dpp4/CD26, Corin, and Dlk1 along with markers of myofibroblasts, revealed accessible chromatin in all fibroblast populations despite their lineage specific transcriptome profiles. These results suggests that accessible chromatin does not always translate to gene expression and that many fibroblast lineage markers reflect a fibroblast state, which includes neonatal papillary, reticular, and myofibroblasts. This analysis also provides a possible explanation as to why these marker genes can be promiscuously expressed in different fibroblast populations under different conditions. Our scATAC-seq analysis also revealed that the functional lineage restriction between dermal papilla and adipocytes fates are regulated by distinct chromatin landscapes. Finally, we have developed a webtool for our multi-omics analysis:
Overall design Trunk skin from 4 wild-type postnatal day 0 mouse littermates were used to generate single-cell suspensions of skin cells. These single-cell suspensions were pooled and parallel scRNA-seq and scATAC-seq experiments were conducted on the same pool of cells. The resulting sequencing data was aligned to the mm10 genome.
Web link
Contributor(s) Thompson SM, Phan QM, Winuthayanon S, Driskell IM, Driskell RR
Citation(s) 34922949
Submission date Nov 19, 2021
Last update date Feb 05, 2024
Contact name Sean Thompson
Organization name Washington State University
Department School of Molecular Biosciences
Lab Driskell Lab
Street address BLS 240
City Pullman
State/province WA
ZIP/Postal code 99164
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (2)
GSM5696148 wild-type neonate scRNA-seq
GSM5696149 wild-type neonate scATAC-seq
BioProject PRJNA781969
SRA SRP346943

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Supplementary file Size Download File type/resource
GSE189210_RAW.tar 5.2 Gb (http)(custom) TAR (of BED, CSV, H5, MTX, TBI, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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