Global skin gene expression profile of early diffuse cutaneous systemic sclerosis shows a prominent innate and adaptive immunity profile

RNA from skin biopsies from 48 patients in the Prospective Registry for Early Systemic Sclerosis (PRESS) cohort (mean disease duration 1.3 years) and 33 matched healthy controls was examined by nextGen RNA sequencing Overall design: 3- or 4-mm diameter punch biopsies were obtained from the forearm skin and immersed in RNAlater solution (Qiagen). RNA was extracted using miRNeasy Mini kits (Qiagen). cDNA libraries were prepared using the Illumina TruSeq stranded Total RNA Library Prep Gold kit, loaded on cBot (Illumina) at a final concentration of 10 pM to perform cluster generation, followed by 2 x 76 bp paired-end sequencing on HiSeq 2500 (Illumina), generating on average around 50 million reads per sample.