Sirna sequence design software

For the luciferase assay, the ATG5 and ATG7 promoter regions (−1510 to −7 and −1538 to -26, respectively) were amplified from genomic DNA using the primer pairs shown in S1 Table and inserted into the pGL3.0-basic vector (Promega, Madison, USA). pOTB7-VCP and pT7T3Pac-MAP1LC3B (Korea Unigene Clone) were subcloned into the pCMV-Flag vector and pEGFP-C1 vector, respectively, and Flag-VCP was subcloned into the plenti-puro vector (Addgene) using primer pairs mentioned in S1 Table. Short hairpin RNAs (shRNAs) against KDM3B and VCP were designed using siRNA sequence design software (Clontech). Double-stranded oligonucleotides for shRNA plasmid construction were produced using primers at the 5′ and 3′ ends (S1 Table). These oligonucleotides were inserted into the AgeI/EcoRI site of the pLKO.1 TRC vector (Addgene).

For the luciferase assay, the IL10RA and RGCC promoter regions (−998 to −1 and −1468 to +5, respectively) were amplified from genomic DNA using the primer pairs shown in S1 Table and inserted into the pGL3.0-basic vector (Promega). pcDNA3-PAX5 was subcloned into the pCMV-Flag vector using primer pairs shown in S1 Table. Short hairpin RNAs (shRNAs) against HDAC2 and PAX5 were designed using siRNA sequence design software (Clontech). Double-stranded oligonucleotides for shRNA plasmid construction were produced using primers at the 5′ and 3′ ends (S1 Table). These oligonucleotides were inserted into the AgeI/EcoRI site of the pLKO.1 TRC vector (Addgene).