4 cell lines depleted of key NMD-factors (SMG5, SMG6 and SMG7)
This dataset comprises 54 RNA libraries generated from four distinct cell lines. The cell lines are HEK293, HeLa, U2OS and MCF7. The goal is to study the effects of Nonsense-Mediated mRNA Decay (NMD) factors depletion. The libraries feature both control samples, utilizing Luciferase-targeting short interference RNAs (siRNA), and samples with specific NMD factors (SMG5, SMG6, SMG7) knocked down or knocked out. Key methodologies employed are siRNA-mediated knockdowns and CRISPR-Cas9 knockouts. A subset of eight libraries, particularly the HEK293 SMG7 KO SMG6 KD comparison, were sequenced using Nanopore Direct RNA Sequencing, in addition to the Illumina sequencing approach. The dataset facilitates comparative analysis across different cell lines and genetic modifications, offering insights into the impact of NMD factor alterations on transcriptome expression and identification of NMD-sensitive transcripts.