Bulk RNA-Seq methods

mRNA-Seq

mRNA-Seq uses poly-dT oligo based enrichment of polyadenylated RNA and is the most frequently applied workflow; for this we require good quality, non-fragmented RNA (RIN values of at least 7, but >9 for optimal quality (see section [Sample quality control and quantification]).

Total RNA-Seq?

Total RNA-Seq using rRNA depletion by probe-based hybridization is suitable for samples with lower RNA integrity (RIN < 7) or when detecting various RNA forms beyond polyadenylated RNAs is desired.
Maintaining not fully processed transcripts in total RNA-Seq can lead to more intronic reads compared to mRNA-Seq, hence requiring sequencing of approximately 20% more reads. This adjustment helps capture a broader range of RNA species and ensures comprehensive coverage of the transcriptome.