Differentially expressed genes in AdV-C5-infected iPSC-derived macrophages in comparison to noninfected control cells

This data set lists differentially expressed genes in human adenovirus C5 (AdV-C5)-infected iPSC-derived macrophages in comparison to noninfected control cells. Two time points post infection, 12 h and 27 h, were analyzed by bulk RNA-seq and cells were infected either with wild type (wt) AdV-C5 or coinfected with wt and a recombinant AdV-C5 virus in which the native E1A enhancer/promoter is replaced by the cytomegalovirus (CMV) immediate early enhancer/promoter (the wtCMV coinfection). Each time point had also a noninfected control sample. The wt virus infection is restricted in the iPSC-derived macrophages, partially due to poor activity of native E1A enhancer/promoter in these cells, whereas the coinfection setting leads to productive infection. Extracted RNA from the cells was prepared for sequencing using Illumina TruSeq Stranded Total RNA kit and ribosomal RNA was depleted with Ribo-Zero rRNA Removal kit. Sequencing was carried out on the Illumina NovaSeq 6000 using the S1 Reagent Kit v1.5. Demultiplexing was performed using the Illumina bcl2fastq Software (v1.10). RNA sequencing analysis was performed using the Sushi framework. Read quality was inspected using FastQC and sequencing adaptors were removed using fastp. Sequencing reads were mapped simultaneously to the GENCODE human genome build GRCh38 patch 13 and the adenovirus 5 (AC_000008.1) genome using the STAR aligner. Counting of gene-level expression values was done using the featureCounts function of the R package Rsubread and differentially expressed genes were analyzed with edgeR Bioconducter package. The raw data from this Bulk RNA-seq have been uploaded to NCBI's Gene Expression Omnibus and are accessible through the accession number GSE317750 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE317750).