Total RNA-seq and long-read RNAseq (Nanopore) upon Son KD in mouse embryonic stem cells

Gene-expression noise can influence cell-fate choices across pathology and physiology. However, a crucial question persists: do regulatory proteins or pathways exist that control noise independently of mean expression levels? Resulting from a previous screen, the protein SON was identified as a potential noise regulator. We perform Son KD and utilize (1) total RNA sequencing (RNA-seq) to analyze differences in splicing efficiency of introns upon Son KD; and (2) Nanopore sequencing to analyze changes in isoform usage. These datasets correspond to the aforementioned total RNA-seq and long-read polyA+ cDNA Nanopore sequencing upon Son KD. Mouse embryonic stem cells (mESCs) were seeded and growth in serum/LIF conditions. 24 hours post-seeding, knock down of Son was induced with siRNA transfection (Lipofectamine 2000). After treatment RNA was extracted and frozen in preparation for RNA sequencing. For total RNA-seq, RNA samples were shipped in dry ice to sequencing company and rRNA depletion and RNA sequencing was performed. Long-read nanopore sequencing was performed in house.