ProtheraCytes transcriptomic analysis
AMI
Total RNA was purified from ProtheraCytes collected from 7 FHD and 8 AMI patients using RNAeasy plus minikit (Qiagen, Courtabeuf, France). Briefly, sample quality was assessed using a DNA High sensitivity chip (Agilent Technologies). Single-end 50 reads barcoded RNA-Seq sequencing library was performed on an Illumina HiSeq4000 with the TruSeq SBS v3 chemistry at iGE3 Genomics Platform (University of Geneva). The normalization and differential expression analysis was performed with the R/Bioconductor package edgeR v.3.28.1, for the genes annotated in the reference genome. Lowly expressed genes were filtered, keeping genes that are expressed at a reasonable level (10 counts in at least 7 samples). The filtered data were normalized by the library size. The differentially expressed genes were estimated with the GLM approach (Generalized Linear Model) using a negative binomial distribution. The genes were considered as differentially expressed when the fold change (FC) was at least twofold with a 5% false discovery rate (FDR) Benjamini–Hochberg multiple testing correction. The raw data was uploaded to GEO (accession# GSE220865).