Recombinant:Article Title: Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag M2 Sigma-Aldrich Cat# F1804-1MG anti-Actinin (H-300) Santa Cruz Biotechnology Cat# sc-15335; RRID: AB_2223809 anti-GAPDH (6C5) Santa Cruz Biotechnology Cat# sc-32233; RRID: AB_627679 anti-myogenin Santa Cruz Biotechnology Cat# sc12732; RRID: AB_627980 anti-myosin This paper N/A anti-mouse Cy3/AlexaFluor488 Jackson ImmunoResearch Cat# 115-165-003 anti-m6A SYSY Cat# 202 003; RRID: AB_2279214 Chemicals, Peptides, and Recombinant Proteins DMEM Sigma-Aldrich Cat# D6546 FBS Sigma-Aldrich Cat# F7524 L-Glutamine Sigma-Aldrich Cat# G7513 EGF Corning Cat# 354052 Penicillin/Streptomycin Sigma-Aldrich Cat# P0781 FGFb Millipore Cat# 01-106 Human Skeletal Muscle DM Promocell Cat# C-23061 Insulin Sigma-Aldrich Cat# 11376497001 Collagen Type I Corning Cat# 354236 Optimem GIBCO Cat# 31985-047 RNase R Epicenter Cat# MRNA092 VILO Superscript Thermo Fisher Scientific Cat# 11754050 SYBR Mastermix QIAGEN Cat# 208052 bis-tris-acrylamide gel Thermo Fisher Scientific Cat# WG1402BOX Embryonic Stem Medium Merck Millipore Cat# SLM-220-B GlutaMAX Thermo Fisher Scientific Cat# 35050-061 LIF Merck Millipore Cat# ESG1107 Advanced D-MEM/F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal Thermo Fisher Scientific Cat# 211030049 KnockOut Serum Replacement Thermo Fisher Scientific Cat# 10828028 B-27 Thermo Fisher Scientific Cat# 17504-044 NE Aminoacids Merck Millipore Cat# TMS-001-C Retinoic Acid Sigma-Aldrich Cat# R2625 Glyoxal loading dye Ambion Cat# AM8551 Mytaq DNA polymerase Bioline Cat# BIO-21105 Cycloheximide Sigma-Aldrich Cat# 01810 RNase guard Thermo Fischer Scientific Cat# N8080119 Qiazol reagent QIAGEN Cat# 79306 Hybond N+ membrane GE Healthcare Cat# RPN303B T7 RNA polymerase Promega Cat# P2077 Proteinase K Thermo Fischer Scientific Cat# 25530049 Puromycin SERVA Cat# 33835.02 Paraformaldehyde Electron microscopy science Cat# 157-8 Goat serum Thermo Fischer Scientific Cat# 16210072 ProLong Diamond reagent Thermo Fischer Scientific Cat# P36930 (Continued on next page) e1 Molecular Cell 66, 22–37.e1–e9, April 6, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich-Aldrich Cat# D9542 FastDigest EcoRI Thermo Fischer Scientific Cat# FD0274 FastDigest NheI Thermo Fischer Scientific Cat# FD0973 BbsI Neb Cat# R0539S FastDigest XbaI Thermo Fischer Scientific Cat# FD0684 NorthernMax buffer Ambion Cat# AM8671 PBS Sigma-Aldrich N/A LDS sample buffer Invitrogen Cat# NP0007 DNase Thermo Fischer Scientific Cat# EN0525 Alkaline Phosphatase Sigma-Aldrich Cat# 000000010713023001 RNase inhibitors Thermo Fischer Scientific Cat# EO0384 T4 Polynucleotide kinase BioLabs Cat# M0236S DMSO Sigma-Aldrich Cat# D4540 T4 RNA Ligase 1 BioLabs Cat# M0204S Lipofectamine 2000 Thermo Fischer Scientific Cat# 11668019 Dharmafect lipid reagent Dharmacon Cat# T-2001-01 Critical Commercial Assays Ribominus technology Thermo Fisher Scientific Cat# A1083708 Real Genomics Genomic DNA extraction kit RBC Bioscience Cat# YGB300 miRNeasy spin columns QIAGEN Cat# 217004 DIG-luminescence detection kit Sigma-Aldrich Cat# 11363514910 DIG-RNA labeling mix Sigma-Aldrich Cat# 000000011277073910 In-Fusion HD Cloning Kit Clontech Cat# 639649 Dynabeads Protein G Immunoprecipitation kit Invitrogen Cat# 10007D 5-Bromo-20-deoxy-uridine Labeling and Detection kit I Sigma-Aldrich Cat# 11296736001 Dual Glo luciferase assay Promega Cat# E2920 Deposited Data RNA sequencing raw data This paper GEO: GSE70389 Experimental Models: Cell Lines Mouse myoblasts C2C12 ATCC Cat# CRL-1772 Human male myoblasts (WT) Telethon Biobank N/A Human male myoblasts (DMD) Telethon Biobank N/A HeLa ATCC Cat# CCL-2 N2A ATCC Cat# CCL-131 Mouse embryonic stem cells This paper N/A Mouse embryonic fibroblasts Millipore Cat# 92590 Oligonucleotides DNA oligonucleotides used in this work are listed in Table S2 siRNAs used in this work are listed in Table S3 Recombinant DNA pcDNA3.1(-) Thermo Fisher Scientific N/A p-circ (name used in this work) Hung Ho Xuan, Gunter Meister Lab N/A p-circ-3xF (name used in this work) Hung Ho Xuan, Gunter Meister Lab N/A circRNA mini vector ZKSCAN1 Addgene #60649 p-circ-3xF D1 This paper N/A p-circ-3xF D2 This paper N/A p-circ-3xF D1-2 This paper N/A (Continued on next page) Molecular Cell 66, 22–37.e1–e9, April 6, 2017 e2
Knock-Out:Article Title: Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag M2 Sigma-Aldrich Cat# F1804-1MG anti-Actinin (H-300) Santa Cruz Biotechnology Cat# sc-15335; RRID: AB_2223809 anti-GAPDH (6C5) Santa Cruz Biotechnology Cat# sc-32233; RRID: AB_627679 anti-myogenin Santa Cruz Biotechnology Cat# sc12732; RRID: AB_627980 anti-myosin This paper N/A anti-mouse Cy3/AlexaFluor488 Jackson ImmunoResearch Cat# 115-165-003 anti-m6A SYSY Cat# 202 003; RRID: AB_2279214 Chemicals, Peptides, and Recombinant Proteins DMEM Sigma-Aldrich Cat# D6546 FBS Sigma-Aldrich Cat# F7524 L-Glutamine Sigma-Aldrich Cat# G7513 EGF Corning Cat# 354052 Penicillin/Streptomycin Sigma-Aldrich Cat# P0781 FGFb Millipore Cat# 01-106 Human Skeletal Muscle DM Promocell Cat# C-23061 Insulin Sigma-Aldrich Cat# 11376497001 Collagen Type I Corning Cat# 354236 Optimem GIBCO Cat# 31985-047 RNase R Epicenter Cat# MRNA092 VILO Superscript Thermo Fisher Scientific Cat# 11754050 SYBR Mastermix QIAGEN Cat# 208052 bis-tris-acrylamide gel Thermo Fisher Scientific Cat# WG1402BOX Embryonic Stem Medium Merck Millipore Cat# SLM-220-B GlutaMAX Thermo Fisher Scientific Cat# 35050-061 LIF Merck Millipore Cat# ESG1107 Advanced D-MEM/F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal Thermo Fisher Scientific Cat# 211030049 KnockOut Serum Replacement Thermo Fisher Scientific Cat# 10828028 B-27 Thermo Fisher Scientific Cat# 17504-044 NE Aminoacids Merck Millipore Cat# TMS-001-C Retinoic Acid Sigma-Aldrich Cat# R2625 Glyoxal loading dye Ambion Cat# AM8551 Mytaq DNA polymerase Bioline Cat# BIO-21105 Cycloheximide Sigma-Aldrich Cat# 01810 RNase guard Thermo Fischer Scientific Cat# N8080119 Qiazol reagent QIAGEN Cat# 79306 Hybond N+ membrane GE Healthcare Cat# RPN303B T7 RNA polymerase Promega Cat# P2077 Proteinase K Thermo Fischer Scientific Cat# 25530049 Puromycin SERVA Cat# 33835.02 Paraformaldehyde Electron microscopy science Cat# 157-8 Goat serum Thermo Fischer Scientific Cat# 16210072 ProLong Diamond reagent Thermo Fischer Scientific Cat# P36930 (Continued on next page) e1 Molecular Cell 66, 22–37.e1–e9, April 6, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich-Aldrich Cat# D9542 FastDigest EcoRI Thermo Fischer Scientific Cat# FD0274 FastDigest NheI Thermo Fischer Scientific Cat# FD0973 BbsI Neb Cat# R0539S FastDigest XbaI Thermo Fischer Scientific Cat# FD0684 NorthernMax buffer Ambion Cat# AM8671 PBS Sigma-Aldrich N/A LDS sample buffer Invitrogen Cat# NP0007 DNase Thermo Fischer Scientific Cat# EN0525 Alkaline Phosphatase Sigma-Aldrich Cat# 000000010713023001 RNase inhibitors Thermo Fischer Scientific Cat# EO0384 T4 Polynucleotide kinase BioLabs Cat# M0236S DMSO Sigma-Aldrich Cat# D4540 T4 RNA Ligase 1 BioLabs Cat# M0204S Lipofectamine 2000 Thermo Fischer Scientific Cat# 11668019 Dharmafect lipid reagent Dharmacon Cat# T-2001-01 Critical Commercial Assays Ribominus technology Thermo Fisher Scientific Cat# A1083708 Real Genomics Genomic DNA extraction kit RBC Bioscience Cat# YGB300 miRNeasy spin columns QIAGEN Cat# 217004 DIG-luminescence detection kit Sigma-Aldrich Cat# 11363514910 DIG-RNA labeling mix Sigma-Aldrich Cat# 000000011277073910 In-Fusion HD Cloning Kit Clontech Cat# 639649 Dynabeads Protein G Immunoprecipitation kit Invitrogen Cat# 10007D 5-Bromo-20-deoxy-uridine Labeling and Detection kit I Sigma-Aldrich Cat# 11296736001 Dual Glo luciferase assay Promega Cat# E2920 Deposited Data RNA sequencing raw data This paper GEO: GSE70389 Experimental Models: Cell Lines Mouse myoblasts C2C12 ATCC Cat# CRL-1772 Human male myoblasts (WT) Telethon Biobank N/A Human male myoblasts (DMD) Telethon Biobank N/A HeLa ATCC Cat# CCL-2 N2A ATCC Cat# CCL-131 Mouse embryonic stem cells This paper N/A Mouse embryonic fibroblasts Millipore Cat# 92590 Oligonucleotides DNA oligonucleotides used in this work are listed in Table S2 siRNAs used in this work are listed in Table S3 Recombinant DNA pcDNA3.1(-) Thermo Fisher Scientific N/A p-circ (name used in this work) Hung Ho Xuan, Gunter Meister Lab N/A p-circ-3xF (name used in this work) Hung Ho Xuan, Gunter Meister Lab N/A circRNA mini vector ZKSCAN1 Addgene #60649 p-circ-3xF D1 This paper N/A p-circ-3xF D2 This paper N/A p-circ-3xF D1-2 This paper N/A (Continued on next page) Molecular Cell 66, 22–37.e1–e9, April 6, 2017 e2
Membrane:Article Title: Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag M2 Sigma-Aldrich Cat# F1804-1MG anti-Actinin (H-300) Santa Cruz Biotechnology Cat# sc-15335; RRID: AB_2223809 anti-GAPDH (6C5) Santa Cruz Biotechnology Cat# sc-32233; RRID: AB_627679 anti-myogenin Santa Cruz Biotechnology Cat# sc12732; RRID: AB_627980 anti-myosin This paper N/A anti-mouse Cy3/AlexaFluor488 Jackson ImmunoResearch Cat# 115-165-003 anti-m6A SYSY Cat# 202 003; RRID: AB_2279214 Chemicals, Peptides, and Recombinant Proteins DMEM Sigma-Aldrich Cat# D6546 FBS Sigma-Aldrich Cat# F7524 L-Glutamine Sigma-Aldrich Cat# G7513 EGF Corning Cat# 354052 Penicillin/Streptomycin Sigma-Aldrich Cat# P0781 FGFb Millipore Cat# 01-106 Human Skeletal Muscle DM Promocell Cat# C-23061 Insulin Sigma-Aldrich Cat# 11376497001 Collagen Type I Corning Cat# 354236 Optimem GIBCO Cat# 31985-047 RNase R Epicenter Cat# MRNA092 VILO Superscript Thermo Fisher Scientific Cat# 11754050 SYBR Mastermix QIAGEN Cat# 208052 bis-tris-acrylamide gel Thermo Fisher Scientific Cat# WG1402BOX Embryonic Stem Medium Merck Millipore Cat# SLM-220-B GlutaMAX Thermo Fisher Scientific Cat# 35050-061 LIF Merck Millipore Cat# ESG1107 Advanced D-MEM/F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal Thermo Fisher Scientific Cat# 211030049 KnockOut Serum Replacement Thermo Fisher Scientific Cat# 10828028 B-27 Thermo Fisher Scientific Cat# 17504-044 NE Aminoacids Merck Millipore Cat# TMS-001-C Retinoic Acid Sigma-Aldrich Cat# R2625 Glyoxal loading dye Ambion Cat# AM8551 Mytaq DNA polymerase Bioline Cat# BIO-21105 Cycloheximide Sigma-Aldrich Cat# 01810 RNase guard Thermo Fischer Scientific Cat# N8080119 Qiazol reagent QIAGEN Cat# 79306 Hybond N+ membrane GE Healthcare Cat# RPN303B T7 RNA polymerase Promega Cat# P2077 Proteinase K Thermo Fischer Scientific Cat# 25530049 Puromycin SERVA Cat# 33835.02 Paraformaldehyde Electron microscopy science Cat# 157-8 Goat serum Thermo Fischer Scientific Cat# 16210072 ProLong Diamond reagent Thermo Fischer Scientific Cat# P36930 (Continued on next page) e1 Molecular Cell 66, 22–37.e1–e9, April 6, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich-Aldrich Cat# D9542 FastDigest EcoRI Thermo Fischer Scientific Cat# FD0274 FastDigest NheI Thermo Fischer Scientific Cat# FD0973 BbsI Neb Cat# R0539S FastDigest XbaI Thermo Fischer Scientific Cat# FD0684 NorthernMax buffer Ambion Cat# AM8671 PBS Sigma-Aldrich N/A LDS sample buffer Invitrogen Cat# NP0007 DNase Thermo Fischer Scientific Cat# EN0525 Alkaline Phosphatase Sigma-Aldrich Cat# 000000010713023001 RNase inhibitors Thermo Fischer Scientific Cat# EO0384 T4 Polynucleotide kinase BioLabs Cat# M0236S DMSO Sigma-Aldrich Cat# D4540 T4 RNA Ligase 1 BioLabs Cat# M0204S Lipofectamine 2000 Thermo Fischer Scientific Cat# 11668019 Dharmafect lipid reagent Dharmacon Cat# T-2001-01 Critical Commercial Assays Ribominus technology Thermo Fisher Scientific Cat# A1083708 Real Genomics Genomic DNA extraction kit RBC Bioscience Cat# YGB300 miRNeasy spin columns QIAGEN Cat# 217004 DIG-luminescence detection kit Sigma-Aldrich Cat# 11363514910 DIG-RNA labeling mix Sigma-Aldrich Cat# 000000011277073910 In-Fusion HD Cloning Kit Clontech Cat# 639649 Dynabeads Protein G Immunoprecipitation kit Invitrogen Cat# 10007D 5-Bromo-20-deoxy-uridine Labeling and Detection kit I Sigma-Aldrich Cat# 11296736001 Dual Glo luciferase assay Promega Cat# E2920 Deposited Data RNA sequencing raw data This paper GEO: GSE70389 Experimental Models: Cell Lines Mouse myoblasts C2C12 ATCC Cat# CRL-1772 Human male myoblasts (WT) Telethon Biobank N/A Human male myoblasts (DMD) Telethon Biobank N/A HeLa ATCC Cat# CCL-2 N2A ATCC Cat# CCL-131 Mouse embryonic stem cells This paper N/A Mouse embryonic fibroblasts Millipore Cat# 92590 Oligonucleotides DNA oligonucleotides used in this work are listed in Table S2 siRNAs used in this work are listed in Table S3 Recombinant DNA pcDNA3.1(-) Thermo Fisher Scientific N/A p-circ (name used in this work) Hung Ho Xuan, Gunter Meister Lab N/A p-circ-3xF (name used in this work) Hung Ho Xuan, Gunter Meister Lab N/A circRNA mini vector ZKSCAN1 Addgene #60649 p-circ-3xF D1 This paper N/A p-circ-3xF D2 This paper N/A p-circ-3xF D1-2 This paper N/A (Continued on next page) Molecular Cell 66, 22–37.e1–e9, April 6, 2017 e2
Electron Microscopy:Article Title: Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Flag M2 Sigma-Aldrich Cat# F1804-1MG anti-Actinin (H-300) Santa Cruz Biotechnology Cat# sc-15335; RRID: AB_2223809 anti-GAPDH (6C5) Santa Cruz Biotechnology Cat# sc-32233; RRID: AB_627679 anti-myogenin Santa Cruz Biotechnology Cat# sc12732; RRID: AB_627980 anti-myosin This paper N/A anti-mouse Cy3/AlexaFluor488 Jackson ImmunoResearch Cat# 115-165-003 anti-m6A SYSY Cat# 202 003; RRID: AB_2279214 Chemicals, Peptides, and Recombinant Proteins DMEM Sigma-Aldrich Cat# D6546 FBS Sigma-Aldrich Cat# F7524 L-Glutamine Sigma-Aldrich Cat# G7513 EGF Corning Cat# 354052 Penicillin/Streptomycin Sigma-Aldrich Cat# P0781 FGFb Millipore Cat# 01-106 Human Skeletal Muscle DM Promocell Cat# C-23061 Insulin Sigma-Aldrich Cat# 11376497001 Collagen Type I Corning Cat# 354236 Optimem GIBCO Cat# 31985-047 RNase R Epicenter Cat# MRNA092 VILO Superscript Thermo Fisher Scientific Cat# 11754050 SYBR Mastermix QIAGEN Cat# 208052 bis-tris-acrylamide gel Thermo Fisher Scientific Cat# WG1402BOX Embryonic Stem Medium Merck Millipore Cat# SLM-220-B GlutaMAX Thermo Fisher Scientific Cat# 35050-061 LIF Merck Millipore Cat# ESG1107 Advanced D-MEM/F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal Thermo Fisher Scientific Cat# 211030049 KnockOut Serum Replacement Thermo Fisher Scientific Cat# 10828028 B-27 Thermo Fisher Scientific Cat# 17504-044 NE Aminoacids Merck Millipore Cat# TMS-001-C Retinoic Acid Sigma-Aldrich Cat# R2625 Glyoxal loading dye Ambion Cat# AM8551 Mytaq DNA polymerase Bioline Cat# BIO-21105 Cycloheximide Sigma-Aldrich Cat# 01810 RNase guard Thermo Fischer Scientific Cat# N8080119 Qiazol reagent QIAGEN Cat# 79306 Hybond N+ membrane GE Healthcare Cat# RPN303B T7 RNA polymerase Promega Cat# P2077 Proteinase K Thermo Fischer Scientific Cat# 25530049 Puromycin SERVA Cat# 33835.02 Paraformaldehyde Electron microscopy science Cat# 157-8 Goat serum Thermo Fischer Scientific Cat# 16210072 ProLong Diamond reagent Thermo Fischer Scientific Cat# P36930 (Continued on next page) e1 Molecular Cell 66, 22–37.e1–e9, April 6, 2017 .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich-Aldrich Cat# D9542 FastDigest EcoRI Thermo Fischer Scientific Cat# FD0274 FastDigest NheI Thermo Fischer Scientific Cat# FD0973 BbsI Neb Cat# R0539S FastDigest XbaI Thermo Fischer Scientific Cat# FD0684 NorthernMax buffer Ambion Cat# AM8671 PBS Sigma-Aldrich N/A LDS sample buffer Invitrogen Cat# NP0007 DNase Thermo Fischer Scientific Cat# EN0525 Alkaline Phosphatase Sigma-Aldrich Cat# 000000010713023001 RNase inhibitors Thermo Fischer Scientific Cat# EO0384 T4 Polynucleotide kinase BioLabs Cat# M0236S DMSO Sigma-Aldrich Cat# D4540 T4 RNA Ligase 1 BioLabs Cat# M0204S Lipofectamine 2000 Thermo Fischer Scientific Cat# 11668019 Dharmafect lipid reagent Dharmacon Cat# T-2001-01 Critical Commercial Assays Ribominus technology Thermo Fisher Scientific Cat# A1083708 Real Genomics Genomic DNA extraction kit RBC Bioscience Cat# YGB300 miRNeasy spin columns QIAGEN Cat# 217004 DIG-luminescence detection kit Sigma-Aldrich Cat# 11363514910 DIG-RNA labeling mix Sigma-Aldrich Cat# 000000011277073910 In-Fusion HD Cloning Kit Clontech Cat# 639649 Dynabeads Protein G Immunoprecipitation kit Invitrogen Cat# 10007D 5-Bromo-20-deoxy-uridine Labeling and Detection kit I Sigma-Aldrich Cat# 11296736001 Dual Glo luciferase assay Promega Cat# E2920 Deposited Data RNA sequencing raw data This paper GEO: GSE70389 Experimental Models: Cell Lines Mouse myoblasts C2C12 ATCC Cat# CRL-1772 Human male myoblasts (WT) Telethon Biobank N/A Human male myoblasts (DMD) Telethon Biobank N/A HeLa ATCC Cat# CCL-2 N2A ATCC Cat# CCL-131 Mouse embryonic stem cells This paper N/A Mouse embryonic fibroblasts Millipore Cat# 92590 Oligonucleotides DNA oligonucleotides used in this work are listed in Table S2 siRNAs used in this work are listed in Table S3 Recombinant DNA pcDNA3.1(-) Thermo Fisher Scientific N/A p-circ (name used in this work) Hung Ho Xuan, Gunter Meister Lab N/A p-circ-3xF (name used in this work) Hung Ho Xuan, Gunter Meister Lab N/A circRNA mini vector ZKSCAN1 Addgene #60649 p-circ-3xF D1 This paper N/A p-circ-3xF D2 This paper N/A p-circ-3xF D1-2 This paper N/A (Continued on next page) Molecular Cell 66, 22–37.e1–e9, April 6, 2017 e2
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