EPC 218 harvested at D0
RNA extraction was performed using Qiagen's RNeasy kit. Library preparation was done unsing Lexogen's QuantSeq 3'mRNA-Seq. Sequencing was performed on an Illumina HiSeq 2500 V4 in high output mode. For data processing, trimming of the Illumina Universal Adapter was performed with cutadapt, before aligning to the human genome (GRCh38) with STAR. featureCounts was used to assign reads to genes as defined by Ensembl. Only genes with at least 100 read counts across samples and at least 2 samples each with a minimum count of 40 were considered in the downstream statistical analysis which was performed in the R environment with the Bioconductor package limma. As samples from the same donor were measured repeatedly over time and cellular state, donor was considered as a random effect in the statistical model and passed to the function duplicateCorrelation as blocking factor. In addition, sequencing batch and sex were modelled as fixed effects to correct for unwanted variation.
NIA-phs004047
DE42NGSUKBR124062