A comparison of gene expression between lesional and non-lesional derived keratinocytes of Hailey-Hailey disease patients.

ABSTRACT: Purpose: The goal of this study was to compare NGS-derived keratinocytes transcriptome profiling (RNA-seq) between non lesional and lesional derived keratinocytes of hailey-Hailey disease patients. Methods: kerationocytes gene profiles of lesional and non-lesional derived keratinocytes were generated by deep sequencing, in triplicate, using Illumina HIseq2000. The sequence reads that passed quality filters were analyzed at gene level with the following methods: STAR for the alignment; HTSeq for generating raw read counts; edgeR for normalization and differential expression analysis. QRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 45 million sequence reads per sample to the human genome (hg19). Hierarchical clustering of gene expressions clearly showed separation between non-lesional and lesional keratinocytes. A total of 1,453 differentially expressed genes at FDR<0.05 were identified, uncovering several genes that may contribute to Hailey-Hailey manifestation function. Conclusions: Our study represents the first detailed analysis of keratinocyte gene expression profile, generated by RNA-seq technology. We conclude that RNA-seq gene based characterization of HHD-keratinocytes would expedite genetic network analyses and permit the dissection of complex biological functions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE77466 | GEO | 2017/02/01

SECONDARY ACCESSION(S): PRJNA310433

REPOSITORIES: GEO