Strong Correlation of Gene Counts and Differentially Expressed Genes Between a 3′ RNA-Seq and RNA Hybridisation Platform in Transcriptome Analyses from Canine Archival Tissue [RNA-Seq]

ABSTRACT: 3' RNA-Seq and direct RNA hybridisation are conceptually different approaches for high throughput transcriptome analysis. The former generates next-generation sequencing libraries by targeting and amplifying 3'-end sequences of 60 to 80 nucleotides in length, whereas the latter quantifies transcripts of 800 pre-selected genes. Since both methods are applicable to short mRNA fragments, they are thought to allow for transcriptome analyses from formalin-fixed, paraffin-embedded (FFPE) archival tissue containing partially degraded RNA. In this study, results of both approaches were compared on sample- and gene-wise count levels, gene expression strength and direction, as well as the overlap of differentially expressed genes (DEGs). Using two different oncological perspectives, i.e. a stage-dependent and entity-contrasting comparison on 35 FFPE canine tumours, both methods proved suitable for their use on archival tissues. A moderately to very strong overall count correlation was found (range of Pearson and Spearman means: 0.66 – 0.87). Of note, the gene-wise count correlations depended on gene expression strength. Finally, in the entity-contrasting comparison, expression direction correlated very strongly (range: 0.88 – 0.91) but DEGs only moderately overlapped (Jaccard index: 0.53). Aside from these figures, different practically relevant aspects of the two technologies offer distinct advantages, depending on the objectives and design of a study.

ORGANISM(S): Canis lupus familiaris

PROVIDER: GSE262022 | GEO | 2024/03/21

REPOSITORIES: GEO