Project includes skin biopsies collected from canine atopic dermatitis affected and healthy German shepherd dogs. Project aimed to define genes with different expression in cases compared controls.

Canine atopic dermatitis (CAD) is a pruritic allergic skin disease. We performed mRNA sequencing of non-lesional axillary skin biopsies from German shepherd dogs: five treated subclinical CAD cases, one untreated mild CAD case, and three healthy controls. Obtained RNA sequences were mapped to the dog genome (CanFam3.1). A high-quality skin transcriptome was generated with 23,510 expressed gene transcripts. Differentially expressed genes (DEGs) were defined by comparing treated CAD cases and an untreated CAD case, respectively, to controls.RNA was isolated using Qiagen RNeasy Mini Kit, Quick-Start Protocol Part 1 and 2 (Jan 2011, www.qiagen.com) with a DNase I digestion step included and the optional step after step 6 in Part 1 excluded (i.e. no new collection tubes were used). Prior to RNA isolation, the beads were washed in 99.9% EtOH for 20 min. and then sprayed with RNaseZap RNase Decontamination Solution (Applied Biosystems, Foster City, CA, USA). Poly-A selected/paired-end libraries and sequencing of 100bp paired-end reads using Illumina HiSeq 2000 were performed at the SNP&SEQ Technology Platform at Science for Life Laboratory, Uppsala University, Sweden. RNA concentration and quality of each sample was assessed at the SNP&SEQ Technology Platform. In total, expression of 23,510 gene transcripts (including 6,440 LOC genes), 48,265 isoforms, 36,295 transcription start sites (TSS), and 23,509 promoters were detected in the dog skin samples. All samples remaining after QC at the sequencing platform passed the threshold of sequence quality (mean PHRED score >31) and aligned reads per sample ranged from 36.8 to 45.6 million.