title: RNA-Seq of homo sapiens: PMM2-CDG patient skin
design: Following cell culture and treatment with or without 10 nm/ml TNF-alpha for 24H at 37ºC, cDNAlibraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen Ghmb). RNA sequencing was performed on the NextSeq500 (Illumina) in a 75-base single-end mode, with a minimum target coverage of 6 million reads per library. The QuantSeq 3' mRNA-Seq Integrated Data Analysis Pipeline from Lexogen GmbH on BlueBee® Genomics Platform was used to obtain the read counts for each gene of each sample. Specifically, the quality control of the RNA-Seq raw data was assessed using the FASTQC (v 0.11.5). Then, the BBDuk software (v 35.92) was used to trim and remove the standard adapter sequences and poly(A) tails. The resulting trimmed reads were aligned with the Genome Reference Consortium human build 38 (GRCh38) reference genome using STAR (v 2.5.2a) and counted with HTSeq.