Transcriptome altered by latent human cytomegalovirus infection on THP-1 cells using RNA-seq.

"the rna-seq reads used in this study have been deposited to ncbi sequence read archive (sra) database under accession number sra458685 2 4 we implement the following four steps to enhance the reliability of constructing expressed lncrnas from transcripts obtained from our two samples: (1) select transcripts with multi-exon; (2)select transcripts which are longer than 200 bases; (3) calculate the coding potential of each transcript using cnci (coding noncoding index) in-house software( ) to recover the transcripts which can be categorized as noncoding (cnci is a powerful signature tool that profiles adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations; cnci software is available at http://www bioinfo org/software/cnci ); (4) select transcripts that are located in the intron intergenic and antisense regions from genes encoding known 2 5 the gene expression was calculated using the rpkm method (reads per kilobase transcriptome per million reads) and a minimum rpkm value of 0 1 is required for expressed genes/isoforms ( )."

"Competing interests The authors have declared that no competing interests exist."

"We thank Prof. JinyuWu for comments and critical reading of this manuscript. This project was supported by grants from the 10.13039/501100001809National Science Foundation of China (No. 81071365) and the 10.13039/501100004731Zhejiang Provincial Natural Science Foundation of China (NO. LY13H190006)."