RNA-seq analysis of T-ALL cells following FTO or ELK3 silencing
FTO serves as one of the demethylases for RNA N (6)-methyladenosine (m6A). ELK3 is responsible for encoding a member within the ETS-domain transcription factor family and the ternary complex factor (TCF) subfamily. To elucidate the roles and mechanisms of FTO and ELK3 in human T-cell acute lymphoblastic leukemia (T-ALL), we conducted RNA-seq analyses in KOPTK1 or CUTLL1 T-ALL cells following the silencing of FTO or ELK3 Overall design: After silencing FTO or ELK3 in T-ALL cells, total RNA extraction was performed using Trizol. Genomic DNA was eliminated through in-solution DNase I treatment (Thermo Scientific). Subsequently, poly (A) mRNA was purified from the total RNA using the Dynabeads mRNA purification kit (Invitrogen). RNA libraries were then constructed using the NEB Next Ultra Directional RNA Library Prep Kit (NEB) and subjected to sequencing as 150 bp paired-end reads on the NovaSeq 6000 platform.