RNA-seq of infected (MC58siaD) choroid plexus epithelial cells
MACE-seq: libraries were prepared with the MACE-Kit for 3-mRNA sequencing (GenXpro, Germany); sequencing was performed on a Nextseq 550 (Illumina, USA) with a High Output Flow Cell, multiplexing all samples with 75 bp reads. After demultiplexing with Casava (Illumina, USA), unique molecular barcodes (UMI) were extracted from each read. The reads were aligned to hg38 with bwa (Li 2013) and reads that had the same position and UMI were collapsed with picard tools (Broad Institute, 2019). The resulting consensus sequences were loaded into CLC Genomics Workbench (Qiagen, Germany), where the tool RNA-Seq Analysis was applied to each sample