Chr18 Transcriptome using RT-qPCR, Illumina HiSeq, and ONT MinION Technologies Applied to the Same Set of HepG2 Cells and Liver Samples
Enigma of the missing proteins and of the functionally uncharacterized proteins lays in the negligence to the transcription of genes. With a focus on Chr18 we have implemented the targeted transcriptome analysis (RT-qPCR), also the shotgun analysis (Illumina HiSeq and Oxford Nanopore Technology, ONT) for the same set of the samples: Liver samples from three post-mortem donors and HepG2 cell line of concordant passages.Up to 250 transcripts encoded in the Chr18 were covered in this study by assembling the data from different nucleotide sequencing or quantitative nucleotide detection technologies. The match between different sources of the transcriptome data was rather poor: slightly above 50% of the expressed genes were simultaneously confirmed by all of the used methods. At the same time the correlations between the expresson datasets showed the disting clustering between source of the biological methods, with group of the similar analytical methodsThe result of the work is the investigation of a compendium of 23 genes from the Chr18, of which 10 were assigned to the uPE1 category, while the rest 13 genes were missing. We compared all of our datasets and selected heat-shock binding protein as the missing one and the C18orf21 as the uPE1 for the analysis in Integrated Genome Viewer. It was observed that proteotypic peptides were mapped at least to three Illumina or ONT reads, which contain no splice junctions or non-synonymous nucleotide mismatches or indels in the collection of liver and HpG2 cell specimens used in this study.