Next Generation Sequencing Facilitates Quantitative Analysis of Cyp26b1-/-skin and En1cre;Cyp26b1f/- epidermal and dermal Transcriptomes

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived skin transcriptome profiling (RNA-seq) to determine pathways and networks dependent on retinoic acid during skin development. Methods: Skin mRNA profiles of embryonic day E16.5 wild-type (WT) and Cyp26b1 knockout (Cyp26b1-/-), and of control and of dermal and epidermal skin fractions of Engrailed1cre;Cyp26b1f/- (En1cre;Cyp26b1f/-) conditional knockout mice were generated by deep sequencing, in duplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level by ANOVA (ANOVA) and TopHat. qRT–PCR validation was performed using TaqMan and SYBR Green assay. Results: RNA-Seq data were generated with Illumina’s HiSeq 2000 system. Raw sequencing data were processed with CASAVA 1.8.2 to generate fastq files. Reads of 50 bases were mapped to the mouse transcriptome and genome mm9 using TopHat 1.3.2. Gene expression values (RPKM) were calculated with Partek Genomics Suite 6.6, which was also used for the ANOVA analysis to determine significantly differentially expressed genes. Conclusions: Our study represents the first detailed analysis of Cyp26b1-/- skin and En1cre;Cyp26b1f/- dermis/epidermic transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Skin mRNA profiles of embryonic-day 16.5 wild type (WT) and Cyp26b1-/- mice and of dermis and epidermis of embryonic day 18.5 control and En1cre;Cyp26b1f/- were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.

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Okano J, Levy C, Lichti U, Sun HW, Yuspa SH, Sakai Y, Morasso MI