Mixed
Standard RNA-seq normalization strategies that ignore global changes in total RNA content during resistance training produce counterintuitive, biologically invalid results by failing to account for increased ribosomal biogenesis and tissue mass.
If you are analyzing muscle gene expression after resistance training, do not use standard normalization methods that assume total RNA remains constant. You must account for the increase in total RNA (ribosomal biogenesis) caused by muscle growth, or your results will be biologically invalid and counterintuitive.
traditional normalization and non-normalized models resulted in counterintuitive reverse dose-dependency for many genes. Overall, training led to robust transcriptome changes... After accounting for the amounts of muscle tissue used in library preparation, global mRNA expression increased by 43–53%.
Why this rating
The study uses a robust within-participant design with 25 participants, multiple time points, and validation against protein expression, though it is a single study.
Source
Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline
Yusuf Khan et al. · BMC Bioinformatics · 2020
DOI 10.1186/s12859-020-03866-y
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