HAP1 WT and MATR3 KO cells were lysed by RNAzol (Sigma, cat#R4533-100ML??) to prepare total RNA for sequencing using the DirectZol RNA miniPrep Plus (ZYMO RESEARCH, CAT#R2072) per manufacturer's instruction. cDNA libraries were prepared with the NEBNext® rRNA Depletion Kit v2  (NEB, E7405L) followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina ( NEB, E7760L) and NEBNext® Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA Set 1) (E7416L). The final library were sequenced on Novaseq6000, Chemistry 1.5V as 100-8-8-100 at the Genomic  Technology Section, NIAMS, NIH.