Skin biopsy RNA-seq sample processing and analysis
SKIN
Skin biopsies were collected, submerged in RNALater within 30 min of collection and incubated overnight at 4 °C. Supernatant was then removed, and the sample was frozen at −20 °C. RNA was extracted from the frozen biopsies using the Qiagen RNeasy Plus Universal Mini Kit (cat. no. 73404). Ribosomal RNA depletion was performed using the Qiagen FastSelect HMR (cat. no. 334375). RNA-seq libraries were prepared using the NEBNext Ultra II RNA library prep kit (cat. no. E7770L). Libraries were sequenced on an Illumina NextSeq 500 sequencer.Raw sequencing data were processed by the standard Illumina software package bcl2fastq to demultiplex the reads and perform base calling.Sequencing reads were trimmed using cutadaptAfter trimming, genes were quantified by pseudoalignment with kallistoDifferential expression analysis was performed using sleuthAnalytical pipelines were implemented using snakemake