Western Blot:Article Title: N 6 -methyladenosine in 28S rRNA promotes oncogenic mRNA translation and tyrosine catabolism.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZCCHC4 Abcam Cat#ab154002 Rabbit polyclonal anti-a-Tubulin Proteintech Cat#10094-1-AP Rabbit polyclonal anti-GAPDH Proteintech Cat#60004-1-Ig; RRID: AB_2107436 Rabbit polyclonal anti-m6A Synaptic Systems Cat#202003; RRID: AB_2279214 Rabbit anti-IgG Proteintech Cat#30000-0-AP Mouse monoclonal anti-Puromycin Millipore Cat# MABE343; RRID: AB_2566826 Rabbit Polyclonal anti-Ki67 Novus Cat#NB500-170; RRID: AB_2756525 Rabbit Polyclonal anti-CK19 Proteintech Cat#10712-1-AP Mouse monoclonal anti-Flag (for WB) Sigma Cat#A8592 Mouse monoclonal anti-Flag (for co-IP) Proteintech Cat#66008-4-IG Rabbit Polyclonal anti-HA Proteintech Cat#51064-2-AP Mouse monoclonal anti-HPD Proteintech Cat67552-1-Ig Rabbit Polyclonal anti-eIF4E Proteintech Cat#11149-1-AP Rabbit Polyclonal anti-eIF3G Proteintech Cat#11165-1-AP Rabbit Polyclonal anti-eIF4G1 Proteintech Cat#15704-1-AP Rabbit Polyclonal anti-BAX Proteintech Cat# 50599-2-Ig Rabbit monoclonal anti-BCL2 Abcam Cat# ab182858 Rabbit polyclonal anti-Caspase-3 Proteintech Cat# 19677-1-AP Rabbit polyclonal anti-RPL24 Proteintech Cat# 17082-1-AP; RRID: AB_2181728 HRP-linked Goat anti-rabbit IgG (H + L) Proteintech Cat# SA00001-2; RRID: AB_2722564 HRP-linked Goat anti-Mouse IgG (H + L) Proteintech Cat# SA00001-1; RRID: AB_2722565 M5 Goat anti-Rabbit IgG, Cy3 Conjugated (594) Meis Cat# MF246-01 Goat anti-mouse IgG H&L (Alexa Fluor 488) Abcam Cat#150113; RRID: AB_2576208 Bacterial and virus strains DH5a Competent cells Thermo Fisher Scientific Cat#18265017 BL21(DE3) competent E. coli New England Biolabs Cat#C25271 Biological samples Frozen human intrahepatic cholangiocarcinoma tissues Sun Yat-sen University Cancer Center N/A Intrahepatic cholangiocarcinoma tissue microarrays Shanghai Outdo Biotech Company HIBDA180SU02 Chemicals, peptides, and recombinant proteins DMEM medium (without tyrosine) Procell DM150220 Enzyme EDTA Nerobasal Cat# S310KJ Penicillin-Streptomycin-Amphotericin B Procell Cat# PB180121 Mycoplasma Elimination Reagent TRANSGEN BIOTECH Cat# FM4-01-02 PEI Proteintech Cat# PR40001 Puromycin Selleck Cat# CL13900 Polybrene YEASEN Cat# 40804ES76 AG RNAex Pro RNA extraction buffer Accurate Biology Cat# AG21101 RIPA Beyotime Cat# P0013B DAPI Solarbio Cat# C0065 Cycloheximide Sigma Cat# C7698 Dithiothreitol Sigma Cat# D0632 (Continued on next page) Cell Reports 44, 115139, January 28, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER MOPS Sigma Cat# M1254 MgCl2 Macklin Cat# M875550 NaCl Macklin Cat# S805277 KCl Sigma Cat# 746436 10X TBE Solarbio Cat# T1051 m-APA Sigma Cat# 498289 MAA Nanjing Xize Pharmaceutical Technology Cat# TYR002 Homogentisate (HGA) Sigma Cat# H0751 4-HPP Sigma Cat# 114286 Urea Sigma Cat# U6504 Protein marker EpiZyme Cat# WJ103L 10% ammonium persulfate Solarbio Cat# A1030 TEMED Beyotime Cat# ST728 40% (39:1) Acr/Bis Beyotime Cat# ST004 Slide-A-Lyzer mini dialysis cup, 10K Thermo Scientific Cat# 88404 Benzamidinium chloride Sigma Cat# 434760 Ni-NTA Agarose Qiagen Cat# 30210 IPTG Sigma Cat# 16758 Imidazole Sigma Cat# 1202 TritonTM X-100 Sigma Cat# 78787 RNasin Ribonuclease Inhibitor Beyotime Cat# P1008 RNaseout Invitrogen Cat# 10777019 BeyoMagTM Streptavidin Magnetic Beads Beyotime Cat# P2151 m7GTP-Agarose Jena Bioscience Cat# AC-155S m7G(50)ppp(50)G Cap Analog Ambion Cat# AM8048 IP lysis buffer Thermo Scientific Cat# 87787 Heparin Sigma Cat# H3393 PMSF Sigma Cat# P7626 Benzamidine Sigma Cat# 434760 RQ1 DNase Promega Cat#M6101 Proteinase K Vazyme Cat# DE102-01 2M Tris-HCl (pH 7.8) Sangon Biotech Cat#B548140 1M Tris-HCl (pH 7.4) Beyotime Cat#ST774 0.5M EDTA (pH 8.0) Beyotime Cat#C0196 IGEPAL CA-630 Beyotime Cat#ST2045 Crystal violet Beyotime Cat# C0121 Bst 2.0 DNA polymerase New England BioLabs Cat# M0537S ATP Takara Cat# 4041 dNTP Takara Cat# 4030 Cutsmart New England Biolabs Cat# B7204S T4 DNA polymerase New England Biolabs Cat# M0203L SplintR ligase New England Biolabs Cat# M0375S AAV2/8-hTBG-iCre virus Taitool Bioscience Cat#S0657-8 L-TYROSINE (13C9, 99%) Cambridge Isotope Laboratories Cat#CLM-2263-H-PK (Continued on next page) 18 Cell Reports 44, 115139, January 28, 2025
Virus:Article Title: N 6 -methyladenosine in 28S rRNA promotes oncogenic mRNA translation and tyrosine catabolism.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZCCHC4 Abcam Cat#ab154002 Rabbit polyclonal anti-a-Tubulin Proteintech Cat#10094-1-AP Rabbit polyclonal anti-GAPDH Proteintech Cat#60004-1-Ig; RRID: AB_2107436 Rabbit polyclonal anti-m6A Synaptic Systems Cat#202003; RRID: AB_2279214 Rabbit anti-IgG Proteintech Cat#30000-0-AP Mouse monoclonal anti-Puromycin Millipore Cat# MABE343; RRID: AB_2566826 Rabbit Polyclonal anti-Ki67 Novus Cat#NB500-170; RRID: AB_2756525 Rabbit Polyclonal anti-CK19 Proteintech Cat#10712-1-AP Mouse monoclonal anti-Flag (for WB) Sigma Cat#A8592 Mouse monoclonal anti-Flag (for co-IP) Proteintech Cat#66008-4-IG Rabbit Polyclonal anti-HA Proteintech Cat#51064-2-AP Mouse monoclonal anti-HPD Proteintech Cat67552-1-Ig Rabbit Polyclonal anti-eIF4E Proteintech Cat#11149-1-AP Rabbit Polyclonal anti-eIF3G Proteintech Cat#11165-1-AP Rabbit Polyclonal anti-eIF4G1 Proteintech Cat#15704-1-AP Rabbit Polyclonal anti-BAX Proteintech Cat# 50599-2-Ig Rabbit monoclonal anti-BCL2 Abcam Cat# ab182858 Rabbit polyclonal anti-Caspase-3 Proteintech Cat# 19677-1-AP Rabbit polyclonal anti-RPL24 Proteintech Cat# 17082-1-AP; RRID: AB_2181728 HRP-linked Goat anti-rabbit IgG (H + L) Proteintech Cat# SA00001-2; RRID: AB_2722564 HRP-linked Goat anti-Mouse IgG (H + L) Proteintech Cat# SA00001-1; RRID: AB_2722565 M5 Goat anti-Rabbit IgG, Cy3 Conjugated (594) Meis Cat# MF246-01 Goat anti-mouse IgG H&L (Alexa Fluor 488) Abcam Cat#150113; RRID: AB_2576208 Bacterial and virus strains DH5a Competent cells Thermo Fisher Scientific Cat#18265017 BL21(DE3) competent E. coli New England Biolabs Cat#C25271 Biological samples Frozen human intrahepatic cholangiocarcinoma tissues Sun Yat-sen University Cancer Center N/A Intrahepatic cholangiocarcinoma tissue microarrays Shanghai Outdo Biotech Company HIBDA180SU02 Chemicals, peptides, and recombinant proteins DMEM medium (without tyrosine) Procell DM150220 Enzyme EDTA Nerobasal Cat# S310KJ Penicillin-Streptomycin-Amphotericin B Procell Cat# PB180121 Mycoplasma Elimination Reagent TRANSGEN BIOTECH Cat# FM4-01-02 PEI Proteintech Cat# PR40001 Puromycin Selleck Cat# CL13900 Polybrene YEASEN Cat# 40804ES76 AG RNAex Pro RNA extraction buffer Accurate Biology Cat# AG21101 RIPA Beyotime Cat# P0013B DAPI Solarbio Cat# C0065 Cycloheximide Sigma Cat# C7698 Dithiothreitol Sigma Cat# D0632 (Continued on next page) Cell Reports 44, 115139, January 28, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER MOPS Sigma Cat# M1254 MgCl2 Macklin Cat# M875550 NaCl Macklin Cat# S805277 KCl Sigma Cat# 746436 10X TBE Solarbio Cat# T1051 m-APA Sigma Cat# 498289 MAA Nanjing Xize Pharmaceutical Technology Cat# TYR002 Homogentisate (HGA) Sigma Cat# H0751 4-HPP Sigma Cat# 114286 Urea Sigma Cat# U6504 Protein marker EpiZyme Cat# WJ103L 10% ammonium persulfate Solarbio Cat# A1030 TEMED Beyotime Cat# ST728 40% (39:1) Acr/Bis Beyotime Cat# ST004 Slide-A-Lyzer mini dialysis cup, 10K Thermo Scientific Cat# 88404 Benzamidinium chloride Sigma Cat# 434760 Ni-NTA Agarose Qiagen Cat# 30210 IPTG Sigma Cat# 16758 Imidazole Sigma Cat# 1202 TritonTM X-100 Sigma Cat# 78787 RNasin Ribonuclease Inhibitor Beyotime Cat# P1008 RNaseout Invitrogen Cat# 10777019 BeyoMagTM Streptavidin Magnetic Beads Beyotime Cat# P2151 m7GTP-Agarose Jena Bioscience Cat# AC-155S m7G(50)ppp(50)G Cap Analog Ambion Cat# AM8048 IP lysis buffer Thermo Scientific Cat# 87787 Heparin Sigma Cat# H3393 PMSF Sigma Cat# P7626 Benzamidine Sigma Cat# 434760 RQ1 DNase Promega Cat#M6101 Proteinase K Vazyme Cat# DE102-01 2M Tris-HCl (pH 7.8) Sangon Biotech Cat#B548140 1M Tris-HCl (pH 7.4) Beyotime Cat#ST774 0.5M EDTA (pH 8.0) Beyotime Cat#C0196 IGEPAL CA-630 Beyotime Cat#ST2045 Crystal violet Beyotime Cat# C0121 Bst 2.0 DNA polymerase New England BioLabs Cat# M0537S ATP Takara Cat# 4041 dNTP Takara Cat# 4030 Cutsmart New England Biolabs Cat# B7204S T4 DNA polymerase New England Biolabs Cat# M0203L SplintR ligase New England Biolabs Cat# M0375S AAV2/8-hTBG-iCre virus Taitool Bioscience Cat#S0657-8 L-TYROSINE (13C9, 99%) Cambridge Isotope Laboratories Cat#CLM-2263-H-PK (Continued on next page) 18 Cell Reports 44, 115139, January 28, 2025
Recombinant:Article Title: N 6 -methyladenosine in 28S rRNA promotes oncogenic mRNA translation and tyrosine catabolism.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZCCHC4 Abcam Cat#ab154002 Rabbit polyclonal anti-a-Tubulin Proteintech Cat#10094-1-AP Rabbit polyclonal anti-GAPDH Proteintech Cat#60004-1-Ig; RRID: AB_2107436 Rabbit polyclonal anti-m6A Synaptic Systems Cat#202003; RRID: AB_2279214 Rabbit anti-IgG Proteintech Cat#30000-0-AP Mouse monoclonal anti-Puromycin Millipore Cat# MABE343; RRID: AB_2566826 Rabbit Polyclonal anti-Ki67 Novus Cat#NB500-170; RRID: AB_2756525 Rabbit Polyclonal anti-CK19 Proteintech Cat#10712-1-AP Mouse monoclonal anti-Flag (for WB) Sigma Cat#A8592 Mouse monoclonal anti-Flag (for co-IP) Proteintech Cat#66008-4-IG Rabbit Polyclonal anti-HA Proteintech Cat#51064-2-AP Mouse monoclonal anti-HPD Proteintech Cat67552-1-Ig Rabbit Polyclonal anti-eIF4E Proteintech Cat#11149-1-AP Rabbit Polyclonal anti-eIF3G Proteintech Cat#11165-1-AP Rabbit Polyclonal anti-eIF4G1 Proteintech Cat#15704-1-AP Rabbit Polyclonal anti-BAX Proteintech Cat# 50599-2-Ig Rabbit monoclonal anti-BCL2 Abcam Cat# ab182858 Rabbit polyclonal anti-Caspase-3 Proteintech Cat# 19677-1-AP Rabbit polyclonal anti-RPL24 Proteintech Cat# 17082-1-AP; RRID: AB_2181728 HRP-linked Goat anti-rabbit IgG (H + L) Proteintech Cat# SA00001-2; RRID: AB_2722564 HRP-linked Goat anti-Mouse IgG (H + L) Proteintech Cat# SA00001-1; RRID: AB_2722565 M5 Goat anti-Rabbit IgG, Cy3 Conjugated (594) Meis Cat# MF246-01 Goat anti-mouse IgG H&L (Alexa Fluor 488) Abcam Cat#150113; RRID: AB_2576208 Bacterial and virus strains DH5a Competent cells Thermo Fisher Scientific Cat#18265017 BL21(DE3) competent E. coli New England Biolabs Cat#C25271 Biological samples Frozen human intrahepatic cholangiocarcinoma tissues Sun Yat-sen University Cancer Center N/A Intrahepatic cholangiocarcinoma tissue microarrays Shanghai Outdo Biotech Company HIBDA180SU02 Chemicals, peptides, and recombinant proteins DMEM medium (without tyrosine) Procell DM150220 Enzyme EDTA Nerobasal Cat# S310KJ Penicillin-Streptomycin-Amphotericin B Procell Cat# PB180121 Mycoplasma Elimination Reagent TRANSGEN BIOTECH Cat# FM4-01-02 PEI Proteintech Cat# PR40001 Puromycin Selleck Cat# CL13900 Polybrene YEASEN Cat# 40804ES76 AG RNAex Pro RNA extraction buffer Accurate Biology Cat# AG21101 RIPA Beyotime Cat# P0013B DAPI Solarbio Cat# C0065 Cycloheximide Sigma Cat# C7698 Dithiothreitol Sigma Cat# D0632 (Continued on next page) Cell Reports 44, 115139, January 28, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER MOPS Sigma Cat# M1254 MgCl2 Macklin Cat# M875550 NaCl Macklin Cat# S805277 KCl Sigma Cat# 746436 10X TBE Solarbio Cat# T1051 m-APA Sigma Cat# 498289 MAA Nanjing Xize Pharmaceutical Technology Cat# TYR002 Homogentisate (HGA) Sigma Cat# H0751 4-HPP Sigma Cat# 114286 Urea Sigma Cat# U6504 Protein marker EpiZyme Cat# WJ103L 10% ammonium persulfate Solarbio Cat# A1030 TEMED Beyotime Cat# ST728 40% (39:1) Acr/Bis Beyotime Cat# ST004 Slide-A-Lyzer mini dialysis cup, 10K Thermo Scientific Cat# 88404 Benzamidinium chloride Sigma Cat# 434760 Ni-NTA Agarose Qiagen Cat# 30210 IPTG Sigma Cat# 16758 Imidazole Sigma Cat# 1202 TritonTM X-100 Sigma Cat# 78787 RNasin Ribonuclease Inhibitor Beyotime Cat# P1008 RNaseout Invitrogen Cat# 10777019 BeyoMagTM Streptavidin Magnetic Beads Beyotime Cat# P2151 m7GTP-Agarose Jena Bioscience Cat# AC-155S m7G(50)ppp(50)G Cap Analog Ambion Cat# AM8048 IP lysis buffer Thermo Scientific Cat# 87787 Heparin Sigma Cat# H3393 PMSF Sigma Cat# P7626 Benzamidine Sigma Cat# 434760 RQ1 DNase Promega Cat#M6101 Proteinase K Vazyme Cat# DE102-01 2M Tris-HCl (pH 7.8) Sangon Biotech Cat#B548140 1M Tris-HCl (pH 7.4) Beyotime Cat#ST774 0.5M EDTA (pH 8.0) Beyotime Cat#C0196 IGEPAL CA-630 Beyotime Cat#ST2045 Crystal violet Beyotime Cat# C0121 Bst 2.0 DNA polymerase New England BioLabs Cat# M0537S ATP Takara Cat# 4041 dNTP Takara Cat# 4030 Cutsmart New England Biolabs Cat# B7204S T4 DNA polymerase New England Biolabs Cat# M0203L SplintR ligase New England Biolabs Cat# M0375S AAV2/8-hTBG-iCre virus Taitool Bioscience Cat#S0657-8 L-TYROSINE (13C9, 99%) Cambridge Isotope Laboratories Cat#CLM-2263-H-PK (Continued on next page) 18 Cell Reports 44, 115139, January 28, 2025
RNA Extraction:Article Title: N 6 -methyladenosine in 28S rRNA promotes oncogenic mRNA translation and tyrosine catabolism.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZCCHC4 Abcam Cat#ab154002 Rabbit polyclonal anti-a-Tubulin Proteintech Cat#10094-1-AP Rabbit polyclonal anti-GAPDH Proteintech Cat#60004-1-Ig; RRID: AB_2107436 Rabbit polyclonal anti-m6A Synaptic Systems Cat#202003; RRID: AB_2279214 Rabbit anti-IgG Proteintech Cat#30000-0-AP Mouse monoclonal anti-Puromycin Millipore Cat# MABE343; RRID: AB_2566826 Rabbit Polyclonal anti-Ki67 Novus Cat#NB500-170; RRID: AB_2756525 Rabbit Polyclonal anti-CK19 Proteintech Cat#10712-1-AP Mouse monoclonal anti-Flag (for WB) Sigma Cat#A8592 Mouse monoclonal anti-Flag (for co-IP) Proteintech Cat#66008-4-IG Rabbit Polyclonal anti-HA Proteintech Cat#51064-2-AP Mouse monoclonal anti-HPD Proteintech Cat67552-1-Ig Rabbit Polyclonal anti-eIF4E Proteintech Cat#11149-1-AP Rabbit Polyclonal anti-eIF3G Proteintech Cat#11165-1-AP Rabbit Polyclonal anti-eIF4G1 Proteintech Cat#15704-1-AP Rabbit Polyclonal anti-BAX Proteintech Cat# 50599-2-Ig Rabbit monoclonal anti-BCL2 Abcam Cat# ab182858 Rabbit polyclonal anti-Caspase-3 Proteintech Cat# 19677-1-AP Rabbit polyclonal anti-RPL24 Proteintech Cat# 17082-1-AP; RRID: AB_2181728 HRP-linked Goat anti-rabbit IgG (H + L) Proteintech Cat# SA00001-2; RRID: AB_2722564 HRP-linked Goat anti-Mouse IgG (H + L) Proteintech Cat# SA00001-1; RRID: AB_2722565 M5 Goat anti-Rabbit IgG, Cy3 Conjugated (594) Meis Cat# MF246-01 Goat anti-mouse IgG H&L (Alexa Fluor 488) Abcam Cat#150113; RRID: AB_2576208 Bacterial and virus strains DH5a Competent cells Thermo Fisher Scientific Cat#18265017 BL21(DE3) competent E. coli New England Biolabs Cat#C25271 Biological samples Frozen human intrahepatic cholangiocarcinoma tissues Sun Yat-sen University Cancer Center N/A Intrahepatic cholangiocarcinoma tissue microarrays Shanghai Outdo Biotech Company HIBDA180SU02 Chemicals, peptides, and recombinant proteins DMEM medium (without tyrosine) Procell DM150220 Enzyme EDTA Nerobasal Cat# S310KJ Penicillin-Streptomycin-Amphotericin B Procell Cat# PB180121 Mycoplasma Elimination Reagent TRANSGEN BIOTECH Cat# FM4-01-02 PEI Proteintech Cat# PR40001 Puromycin Selleck Cat# CL13900 Polybrene YEASEN Cat# 40804ES76 AG RNAex Pro RNA extraction buffer Accurate Biology Cat# AG21101 RIPA Beyotime Cat# P0013B DAPI Solarbio Cat# C0065 Cycloheximide Sigma Cat# C7698 Dithiothreitol Sigma Cat# D0632 (Continued on next page) Cell Reports 44, 115139, January 28, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER MOPS Sigma Cat# M1254 MgCl2 Macklin Cat# M875550 NaCl Macklin Cat# S805277 KCl Sigma Cat# 746436 10X TBE Solarbio Cat# T1051 m-APA Sigma Cat# 498289 MAA Nanjing Xize Pharmaceutical Technology Cat# TYR002 Homogentisate (HGA) Sigma Cat# H0751 4-HPP Sigma Cat# 114286 Urea Sigma Cat# U6504 Protein marker EpiZyme Cat# WJ103L 10% ammonium persulfate Solarbio Cat# A1030 TEMED Beyotime Cat# ST728 40% (39:1) Acr/Bis Beyotime Cat# ST004 Slide-A-Lyzer mini dialysis cup, 10K Thermo Scientific Cat# 88404 Benzamidinium chloride Sigma Cat# 434760 Ni-NTA Agarose Qiagen Cat# 30210 IPTG Sigma Cat# 16758 Imidazole Sigma Cat# 1202 TritonTM X-100 Sigma Cat# 78787 RNasin Ribonuclease Inhibitor Beyotime Cat# P1008 RNaseout Invitrogen Cat# 10777019 BeyoMagTM Streptavidin Magnetic Beads Beyotime Cat# P2151 m7GTP-Agarose Jena Bioscience Cat# AC-155S m7G(50)ppp(50)G Cap Analog Ambion Cat# AM8048 IP lysis buffer Thermo Scientific Cat# 87787 Heparin Sigma Cat# H3393 PMSF Sigma Cat# P7626 Benzamidine Sigma Cat# 434760 RQ1 DNase Promega Cat#M6101 Proteinase K Vazyme Cat# DE102-01 2M Tris-HCl (pH 7.8) Sangon Biotech Cat#B548140 1M Tris-HCl (pH 7.4) Beyotime Cat#ST774 0.5M EDTA (pH 8.0) Beyotime Cat#C0196 IGEPAL CA-630 Beyotime Cat#ST2045 Crystal violet Beyotime Cat# C0121 Bst 2.0 DNA polymerase New England BioLabs Cat# M0537S ATP Takara Cat# 4041 dNTP Takara Cat# 4030 Cutsmart New England Biolabs Cat# B7204S T4 DNA polymerase New England Biolabs Cat# M0203L SplintR ligase New England Biolabs Cat# M0375S AAV2/8-hTBG-iCre virus Taitool Bioscience Cat#S0657-8 L-TYROSINE (13C9, 99%) Cambridge Isotope Laboratories Cat#CLM-2263-H-PK (Continued on next page) 18 Cell Reports 44, 115139, January 28, 2025
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