Western Blot:Article Title: Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution
Article Snippet: .. The following antibodies were used in this study: rabbit monoclonal anti-NDUFS2, clone EPR16266 (abcam, catalog no. ab192022, 1:1,000), mouse monoclonal anti-GAPDH, clone 0411 (Santa Cruz, catalog no. sc-47724, 1:1,000), rabbit polyclonal anti-SELENOF (My BioSource, catalog no. MBS3208942, 1:500), mouse monoclonal anti-UBE2E3, clone OTI7E8 (Novus Biologicals, catalog no. NBP2-03819, 1:500), rabbit polyclonal anti-PPP1R2 (Thermo Fisher Scientific, catalog no. PA5-115787, 1:500), rabbit polyclonal anti-NT5C3 (Proteintech, catalog no. 11393-1-AP, 1:500), rabbit polyclonal anti-SZRD1 (Thermo Fisher Scientific, catalog no. A304-742A, 1:1,000), rabbit polyclonal anti-SNRPD1 (Novus Biologicals, catalog no. NBP2-36427, 1:500), rabbit polyclonal anti-DNAJC19 (Thermo Fisher Scientific, catalog no. PA5-98770, 1:1,000), rabbit polyclonal anti-MAPKAP1 (Proteintech, catalog no. 15463-1-AP, 1:500), rabbit monoclonal anti-CD52, clone EPR3153(2) (abcam, catalog no. ab125071, 1:1,000), rabbit polyclonal anti-A2LD1 (Proteintech, catalog no. 23280-1-AP, 1:500), anti-rabbit IgG, horseradish peroxidase (HRP)-linked antibody (Cell Signaling, catalog no. 7074S WB, 1:2,000), anti-mouse IgG, HRP-linked antibody (Cell Signaling catalog no. 7076S, WB 1:2,000). .. For transient transfection, cells were transfected with casRx (Addgene catalog no. 109053) gRNA construct and pCMV-TRUB1-dCas13D by Lipofectamine 2000 Transfection Reagent (Invitrogen) according to manufacturer’s protocol, or with siRNA by Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following commercial protocols.
Article Title: Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Article Snippet: .. The following antibodies were used in this study: rabbit monoclonal anti-NDUFS2, clone EPR16266 (abcam, catalog no. ab192022, 1:1,000), mouse monoclonal anti-GAPDH, clone 0411 (Santa Cruz, catalog no. sc-47724, 1:1,000), rabbit polyclonal anti-SELENOF (My BioSource, catalog no. MBS3208942, 1:500), mouse monoclonal anti-UBE2E3, clone OTI7E8 (Novus Biologicals, catalog no. NBP2-03819, 1:500), rabbit polyclonal anti-PPP1R2 (Thermo Fisher Scientific, catalog no. PA5-115787, 1:500), rabbit polyclonal anti-NT5C3 (Proteintech, catalog no. 11393-1-AP, 1:500), rabbit polyclonal anti-SZRD1 (Thermo Fisher Scientific, catalog no. A304-742A, 1:1,000), rabbit polyclonal anti-SNRPD1 (Novus Biologicals, catalog no. NBP2-36427, 1:500), rabbit polyclonal anti-DNAJC19 (Thermo Fisher Scientific, catalog no. PA5-98770, 1:1,000), rabbit polyclonal anti-MAPKAP1 (Proteintech, catalog no. 15463-1-AP, 1:500), rabbit monoclonal anti-CD52, clone EPR3153(2) (abcam, catalog no. ab125071, 1:1,000), rabbit polyclonal anti-A2LD1 (Proteintech, catalog no. 23280-1-AP, 1:500), anti-rabbit IgG, horseradish peroxidase (HRP)-linked antibody (Cell Signaling, catalog no. 7074S WB, 1:2,000), anti-mouse IgG, HRP-linked antibody (Cell Signaling catalog no. 7076S, WB 1:2,000). shRNA knockdown and plasmid transfection For transient transfection, cells were transfected with casRx (Addgene catalog no. 109053) gRNA construct and pCMV-TRUB1-dCas13D by Lipofectamine 2000 Transfection Reagent (Invitrogen) according to manufacturer’s protocol, or with siRNA by Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following commercial protocols. .. For lentivirus production, a lentiviral construct (pLKO-Tet-On for inducible knockdown of pseudouridine synthetases, or green fluorescent protein as a negative control) together with pMD2.G (Addgene catalog no. 12259) and psPAX2 (Addgene catalog no. 12260) were cotransfected into 293TN cells (System Biosciences) as previously described47.
shRNA:Article Title: Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Article Snippet: .. The following antibodies were used in this study: rabbit monoclonal anti-NDUFS2, clone EPR16266 (abcam, catalog no. ab192022, 1:1,000), mouse monoclonal anti-GAPDH, clone 0411 (Santa Cruz, catalog no. sc-47724, 1:1,000), rabbit polyclonal anti-SELENOF (My BioSource, catalog no. MBS3208942, 1:500), mouse monoclonal anti-UBE2E3, clone OTI7E8 (Novus Biologicals, catalog no. NBP2-03819, 1:500), rabbit polyclonal anti-PPP1R2 (Thermo Fisher Scientific, catalog no. PA5-115787, 1:500), rabbit polyclonal anti-NT5C3 (Proteintech, catalog no. 11393-1-AP, 1:500), rabbit polyclonal anti-SZRD1 (Thermo Fisher Scientific, catalog no. A304-742A, 1:1,000), rabbit polyclonal anti-SNRPD1 (Novus Biologicals, catalog no. NBP2-36427, 1:500), rabbit polyclonal anti-DNAJC19 (Thermo Fisher Scientific, catalog no. PA5-98770, 1:1,000), rabbit polyclonal anti-MAPKAP1 (Proteintech, catalog no. 15463-1-AP, 1:500), rabbit monoclonal anti-CD52, clone EPR3153(2) (abcam, catalog no. ab125071, 1:1,000), rabbit polyclonal anti-A2LD1 (Proteintech, catalog no. 23280-1-AP, 1:500), anti-rabbit IgG, horseradish peroxidase (HRP)-linked antibody (Cell Signaling, catalog no. 7074S WB, 1:2,000), anti-mouse IgG, HRP-linked antibody (Cell Signaling catalog no. 7076S, WB 1:2,000). shRNA knockdown and plasmid transfection For transient transfection, cells were transfected with casRx (Addgene catalog no. 109053) gRNA construct and pCMV-TRUB1-dCas13D by Lipofectamine 2000 Transfection Reagent (Invitrogen) according to manufacturer’s protocol, or with siRNA by Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following commercial protocols. .. For lentivirus production, a lentiviral construct (pLKO-Tet-On for inducible knockdown of pseudouridine synthetases, or green fluorescent protein as a negative control) together with pMD2.G (Addgene catalog no. 12259) and psPAX2 (Addgene catalog no. 12260) were cotransfected into 293TN cells (System Biosciences) as previously described47.
Knockdown:Article Title: Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Article Snippet: .. The following antibodies were used in this study: rabbit monoclonal anti-NDUFS2, clone EPR16266 (abcam, catalog no. ab192022, 1:1,000), mouse monoclonal anti-GAPDH, clone 0411 (Santa Cruz, catalog no. sc-47724, 1:1,000), rabbit polyclonal anti-SELENOF (My BioSource, catalog no. MBS3208942, 1:500), mouse monoclonal anti-UBE2E3, clone OTI7E8 (Novus Biologicals, catalog no. NBP2-03819, 1:500), rabbit polyclonal anti-PPP1R2 (Thermo Fisher Scientific, catalog no. PA5-115787, 1:500), rabbit polyclonal anti-NT5C3 (Proteintech, catalog no. 11393-1-AP, 1:500), rabbit polyclonal anti-SZRD1 (Thermo Fisher Scientific, catalog no. A304-742A, 1:1,000), rabbit polyclonal anti-SNRPD1 (Novus Biologicals, catalog no. NBP2-36427, 1:500), rabbit polyclonal anti-DNAJC19 (Thermo Fisher Scientific, catalog no. PA5-98770, 1:1,000), rabbit polyclonal anti-MAPKAP1 (Proteintech, catalog no. 15463-1-AP, 1:500), rabbit monoclonal anti-CD52, clone EPR3153(2) (abcam, catalog no. ab125071, 1:1,000), rabbit polyclonal anti-A2LD1 (Proteintech, catalog no. 23280-1-AP, 1:500), anti-rabbit IgG, horseradish peroxidase (HRP)-linked antibody (Cell Signaling, catalog no. 7074S WB, 1:2,000), anti-mouse IgG, HRP-linked antibody (Cell Signaling catalog no. 7076S, WB 1:2,000). shRNA knockdown and plasmid transfection For transient transfection, cells were transfected with casRx (Addgene catalog no. 109053) gRNA construct and pCMV-TRUB1-dCas13D by Lipofectamine 2000 Transfection Reagent (Invitrogen) according to manufacturer’s protocol, or with siRNA by Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following commercial protocols. .. For lentivirus production, a lentiviral construct (pLKO-Tet-On for inducible knockdown of pseudouridine synthetases, or green fluorescent protein as a negative control) together with pMD2.G (Addgene catalog no. 12259) and psPAX2 (Addgene catalog no. 12260) were cotransfected into 293TN cells (System Biosciences) as previously described47.
Plasmid Preparation:Article Title: Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Article Snippet: .. The following antibodies were used in this study: rabbit monoclonal anti-NDUFS2, clone EPR16266 (abcam, catalog no. ab192022, 1:1,000), mouse monoclonal anti-GAPDH, clone 0411 (Santa Cruz, catalog no. sc-47724, 1:1,000), rabbit polyclonal anti-SELENOF (My BioSource, catalog no. MBS3208942, 1:500), mouse monoclonal anti-UBE2E3, clone OTI7E8 (Novus Biologicals, catalog no. NBP2-03819, 1:500), rabbit polyclonal anti-PPP1R2 (Thermo Fisher Scientific, catalog no. PA5-115787, 1:500), rabbit polyclonal anti-NT5C3 (Proteintech, catalog no. 11393-1-AP, 1:500), rabbit polyclonal anti-SZRD1 (Thermo Fisher Scientific, catalog no. A304-742A, 1:1,000), rabbit polyclonal anti-SNRPD1 (Novus Biologicals, catalog no. NBP2-36427, 1:500), rabbit polyclonal anti-DNAJC19 (Thermo Fisher Scientific, catalog no. PA5-98770, 1:1,000), rabbit polyclonal anti-MAPKAP1 (Proteintech, catalog no. 15463-1-AP, 1:500), rabbit monoclonal anti-CD52, clone EPR3153(2) (abcam, catalog no. ab125071, 1:1,000), rabbit polyclonal anti-A2LD1 (Proteintech, catalog no. 23280-1-AP, 1:500), anti-rabbit IgG, horseradish peroxidase (HRP)-linked antibody (Cell Signaling, catalog no. 7074S WB, 1:2,000), anti-mouse IgG, HRP-linked antibody (Cell Signaling catalog no. 7076S, WB 1:2,000). shRNA knockdown and plasmid transfection For transient transfection, cells were transfected with casRx (Addgene catalog no. 109053) gRNA construct and pCMV-TRUB1-dCas13D by Lipofectamine 2000 Transfection Reagent (Invitrogen) according to manufacturer’s protocol, or with siRNA by Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following commercial protocols. .. For lentivirus production, a lentiviral construct (pLKO-Tet-On for inducible knockdown of pseudouridine synthetases, or green fluorescent protein as a negative control) together with pMD2.G (Addgene catalog no. 12259) and psPAX2 (Addgene catalog no. 12260) were cotransfected into 293TN cells (System Biosciences) as previously described47.
Transfection:Article Title: Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Article Snippet: .. The following antibodies were used in this study: rabbit monoclonal anti-NDUFS2, clone EPR16266 (abcam, catalog no. ab192022, 1:1,000), mouse monoclonal anti-GAPDH, clone 0411 (Santa Cruz, catalog no. sc-47724, 1:1,000), rabbit polyclonal anti-SELENOF (My BioSource, catalog no. MBS3208942, 1:500), mouse monoclonal anti-UBE2E3, clone OTI7E8 (Novus Biologicals, catalog no. NBP2-03819, 1:500), rabbit polyclonal anti-PPP1R2 (Thermo Fisher Scientific, catalog no. PA5-115787, 1:500), rabbit polyclonal anti-NT5C3 (Proteintech, catalog no. 11393-1-AP, 1:500), rabbit polyclonal anti-SZRD1 (Thermo Fisher Scientific, catalog no. A304-742A, 1:1,000), rabbit polyclonal anti-SNRPD1 (Novus Biologicals, catalog no. NBP2-36427, 1:500), rabbit polyclonal anti-DNAJC19 (Thermo Fisher Scientific, catalog no. PA5-98770, 1:1,000), rabbit polyclonal anti-MAPKAP1 (Proteintech, catalog no. 15463-1-AP, 1:500), rabbit monoclonal anti-CD52, clone EPR3153(2) (abcam, catalog no. ab125071, 1:1,000), rabbit polyclonal anti-A2LD1 (Proteintech, catalog no. 23280-1-AP, 1:500), anti-rabbit IgG, horseradish peroxidase (HRP)-linked antibody (Cell Signaling, catalog no. 7074S WB, 1:2,000), anti-mouse IgG, HRP-linked antibody (Cell Signaling catalog no. 7076S, WB 1:2,000). shRNA knockdown and plasmid transfection For transient transfection, cells were transfected with casRx (Addgene catalog no. 109053) gRNA construct and pCMV-TRUB1-dCas13D by Lipofectamine 2000 Transfection Reagent (Invitrogen) according to manufacturer’s protocol, or with siRNA by Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following commercial protocols. .. For lentivirus production, a lentiviral construct (pLKO-Tet-On for inducible knockdown of pseudouridine synthetases, or green fluorescent protein as a negative control) together with pMD2.G (Addgene catalog no. 12259) and psPAX2 (Addgene catalog no. 12260) were cotransfected into 293TN cells (System Biosciences) as previously described47.
Construct:Article Title: Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Article Snippet: .. The following antibodies were used in this study: rabbit monoclonal anti-NDUFS2, clone EPR16266 (abcam, catalog no. ab192022, 1:1,000), mouse monoclonal anti-GAPDH, clone 0411 (Santa Cruz, catalog no. sc-47724, 1:1,000), rabbit polyclonal anti-SELENOF (My BioSource, catalog no. MBS3208942, 1:500), mouse monoclonal anti-UBE2E3, clone OTI7E8 (Novus Biologicals, catalog no. NBP2-03819, 1:500), rabbit polyclonal anti-PPP1R2 (Thermo Fisher Scientific, catalog no. PA5-115787, 1:500), rabbit polyclonal anti-NT5C3 (Proteintech, catalog no. 11393-1-AP, 1:500), rabbit polyclonal anti-SZRD1 (Thermo Fisher Scientific, catalog no. A304-742A, 1:1,000), rabbit polyclonal anti-SNRPD1 (Novus Biologicals, catalog no. NBP2-36427, 1:500), rabbit polyclonal anti-DNAJC19 (Thermo Fisher Scientific, catalog no. PA5-98770, 1:1,000), rabbit polyclonal anti-MAPKAP1 (Proteintech, catalog no. 15463-1-AP, 1:500), rabbit monoclonal anti-CD52, clone EPR3153(2) (abcam, catalog no. ab125071, 1:1,000), rabbit polyclonal anti-A2LD1 (Proteintech, catalog no. 23280-1-AP, 1:500), anti-rabbit IgG, horseradish peroxidase (HRP)-linked antibody (Cell Signaling, catalog no. 7074S WB, 1:2,000), anti-mouse IgG, HRP-linked antibody (Cell Signaling catalog no. 7076S, WB 1:2,000). shRNA knockdown and plasmid transfection For transient transfection, cells were transfected with casRx (Addgene catalog no. 109053) gRNA construct and pCMV-TRUB1-dCas13D by Lipofectamine 2000 Transfection Reagent (Invitrogen) according to manufacturer’s protocol, or with siRNA by Lipofectamine RNAiMAX Transfection Reagent (Invitrogen) following commercial protocols. .. For lentivirus production, a lentiviral construct (pLKO-Tet-On for inducible knockdown of pseudouridine synthetases, or green fluorescent protein as a negative control) together with pMD2.G (Addgene catalog no. 12259) and psPAX2 (Addgene catalog no. 12260) were cotransfected into 293TN cells (System Biosciences) as previously described47.
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