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Series GSE113619 Query DataSets for GSE113619
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 [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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 RNA-seq of keloid or healthy control skin.
Contributor(s) Onoufriadis A, Hsu CK, 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
BioProject PRJNA448679
Submission date Apr 24, 2018
Last update date Mar 27, 2019
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 (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (64)
GSM3110282 K1-1st_S021
GSM3110283 K2-1st_S021
GSM3110284 K3-1st_S021
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
SRA SRP137071

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

Supplementary file Size Download File type/resource
GSE113619_RNA-seq_keloids_normalized.csv.gz 872.6 Kb (ftp)(http) CSV
GSE113619_RNA-seq_keloids_raw.csv.gz 821.4 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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