RNA-sequencing of CD56dim NK cells from atopic dermatitis and control patients

Purpose: To determine the underlying transcriptional differences between CD56dim NK cells from atopic dermatitis patients Methods: We sort-purified 30-100,000 CD56dim NK cells from freshly thawed, cryopreserved PBMCs of atopic dermatitis patients and patients undergoing Mohs surgeries. Ribosomal RNA was removed and cDNA was generated with the SMARTer kit (CloneTech) with 10 ng of total RNA per sample. Samples were sequenced to an average depth of 34 million 1x50 reads on a HiSeq3000 (Illumina). Reads were aligned to Ensembl release 76 using STAR, gene counts were determined with Subread:featureCount, and sequence performance was assessed with RSeQC. Overall design: 5 atopic dermatitis patients and 5 control patients were sorted and sequenced, then their transcriptomes were compared to each other using DESeq2 in R v3.5.1 with a single-variable design. Alpha was set to 0.05