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Series GSE113620 Query DataSets for GSE113620
Status Public on Jun 29, 2018
Title Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation [miRNA]
Platform organism synthetic construct
Sample organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary Keloids represent a common form of exaggerated wound scarring that cause considerable morbidity. Moreover, there are limited data on molecular mechanisms underlying keloids and effective therapies are lacking. To gain new insight in the transcriptomic alterations of wound healing in keloid-prone individuals, we followed an integrative approach of RNA-Seq and miRNA expression data analysis in serial skin biopsies of the same site (baseline and six weeks after wounding) in keloid-prone (n=8) and healthy matched control individuals (n=6). Bioinformatic analysis identified 37 miRNAs and 1449 genes that are differentially expressed specifically in keloid-prone individuals during wound healing. Pathway enrichment analysis was undertaken in the RNA-Seq data and identified NOTCH signaling, MAPK signaling, and Toll-like receptor pathways to be altered in keloid-prone individuals after wounding. In addition, dysregulation of DNA repair, p53 signalling and metabolic pathways (RNA, protein, fructose, mannose and glycerophospholipid metabolism) was highlighted during keloid formation. Gene association network analysis demonstrated divergent average expression profiles of cytokine signaling genes, as well as lipid metabolism genes between keloid-prone and healthy individuals during wound healing. In summary, our study provides a comprehensive and integrative analysis of the keloid transcriptome and miRNAome and highlights biological pathways that feature during keloid formation.
Overall design miRNA gene expression profiling skin biopsies at baseline and 6 weeks after wounding in keloid-prone and healthy individuals.
Contributor(s) Onoufriadis A, Hsu C, Ainali C, Ung CY, Rashidghamat E, Yang H, Huang H, Niazi U, Yang J, Nuamah R, Saxena A, de Rinaldis E, McGrath JA
Citation(s) 29870686
Submission date Apr 24, 2018
Last update date Dec 05, 2018
Contact name John Alexander McGrath
Organization name King's College London
Department St John's Institute of Dermatology
Lab St John's Institute of Dermatology
Street address Great Maze Pond
City London
ZIP/Postal code SE1 9RT
Country United Kingdom
Platforms (1)
GPL19117 [miRNA-4] Affymetrix Multispecies miRNA-4 Array
Samples (27)
GSM3110346 Keloid 1 - Day 0_miRNA
GSM3110347 Keloid 2 - Day 0_miRNA
GSM3110348 Keloid 3 - Day 0_miRNA
This SubSeries is part of SuperSeries:
GSE113621 Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation
BioProject PRJNA478484

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE113620_RAW.tar 19.9 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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