Table 1.
Viral genome reference used for detection of viral sequences in CCLE RNA-Seq and WES datasets.
Table 2.
Number of RNA-Seq reads showing complete homology to viral reference sequences.
Table 3.
HTLV-1 reads aligned to HTLV-1 sequences of the NCBI sequence data base.
Table 4.
HTLV-1, HHV-8, and SMRV specific read numbers of cell lines ordered by CCLE file names.
Fig 1.
Virus detection in the cell line BL-70 applying the Taxonomer bioinformatics tool before and after trimming.
Shown are analysis outputs of quick analyses of 213,249 reads. Of those, 125,509 reads (59%) were classified to the human, bacterial, and viral bins (numbers in barackets). A) The table lists all reads categorized to the viral bin before trimming. The reads with a taxonomic level higher than 1 are depicted in the circular diagram. B) The table lists the remaining viral reads after trimming the reads using the Trimmomatic tool (SLIDINGWINDOW:4:30; MINLEN:80) and the two classified viral reads in the circle.
Table 5.
Comparison of read numbers assigned to the viruses and bacteria bins before and after trimming the RNA seq data sets.
Table 6.
BL-70 RNA-Seq reads from the Taxonomer virus bin assigned to virus species or genera.
Fig 2.
Virus detection in the hepatitis B positive cell line Hep_3B2.1–7 applying the Taxonomer bioinformatics tool before and after trimming.
Shown are analysis outputs of quick analyses of 210,769 reads. Of those, 125,462 reads (60%) were classified within the human, bacterial, and viral bins (numbers in brackets). A) The table lists all reads categorized to the viral bin before trimming. The reads with a taxonomic level higher than 1 are depicted in the circular diagram. B) The table lists the remaining viral reads after trimming the reads using the Trimmomatic tool (SLIDINGWINDOW:4:30; MINLEN:80) and the nine consistently classified HBV reads in the circle.
Fig 3.
Shown is an ethidium bromide-stained gel containing the reaction products following PCR amplification with the primers QB-F1-1 and BPyV-rev. A product of 421 bp was obtained. Genomic DNA of the BPyV positive cell line SK-BR-3 and of the BPyV negative human liver cell line SNU-886 were used for the detection. The PCR product of SK-BR-3 was subsequently sequenced and aligned to BPyV sequences of the NCBI nucleotide database showing complete homology.