Reverse Transcription:Article Title: rRNA intermediates coordinate the formation of nucleolar vacuoles in C. elegans.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays GoScript Reverse Transcription System Promega Cat#A5000/A50001 SYBR Green Vazyme Cat#Q111-02/03 ClonExpress MultiS One Step Cloning Kit Vazyme Cat#C113-02 T4 RNA ligase I (ssRNA Ligase) BioLabs Cat#M0204SVIAL Actinomycin D MCE Cat#HY-17559 SYTO RNASelect Green Invitrogen Cat#S32703 Experimental models: Organisms/strains C. elegans Strains, see Table S2 This Paper N/A Oligonucleotides Sequences of double-strand RNA for RNAi, see Table S3 This Paper N/A Primers for ectopic transgenes construction, see Table S4 This Paper N/A Primers for in situ transgenes construction, see Table S5 This Paper N/A Sequences for sgRNA-mediated gene editing, see Table S6 This Paper N/A Primers for cRT and qRT assays, see Table S7 This Paper N/A Other Selected rRNA processing and ribosome assembly factors tested by RNAi screening, see Table S1 This Paper N/A ..
SYBR Green Assay:Article Title: rRNA intermediates coordinate the formation of nucleolar vacuoles in C. elegans.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays GoScript Reverse Transcription System Promega Cat#A5000/A50001 SYBR Green Vazyme Cat#Q111-02/03 ClonExpress MultiS One Step Cloning Kit Vazyme Cat#C113-02 T4 RNA ligase I (ssRNA Ligase) BioLabs Cat#M0204SVIAL Actinomycin D MCE Cat#HY-17559 SYTO RNASelect Green Invitrogen Cat#S32703 Experimental models: Organisms/strains C. elegans Strains, see Table S2 This Paper N/A Oligonucleotides Sequences of double-strand RNA for RNAi, see Table S3 This Paper N/A Primers for ectopic transgenes construction, see Table S4 This Paper N/A Primers for in situ transgenes construction, see Table S5 This Paper N/A Sequences for sgRNA-mediated gene editing, see Table S6 This Paper N/A Primers for cRT and qRT assays, see Table S7 This Paper N/A Other Selected rRNA processing and ribosome assembly factors tested by RNAi screening, see Table S1 This Paper N/A ..
Cloning:Article Title: rRNA intermediates coordinate the formation of nucleolar vacuoles in C. elegans.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays GoScript Reverse Transcription System Promega Cat#A5000/A50001 SYBR Green Vazyme Cat#Q111-02/03 ClonExpress MultiS One Step Cloning Kit Vazyme Cat#C113-02 T4 RNA ligase I (ssRNA Ligase) BioLabs Cat#M0204SVIAL Actinomycin D MCE Cat#HY-17559 SYTO RNASelect Green Invitrogen Cat#S32703 Experimental models: Organisms/strains C. elegans Strains, see Table S2 This Paper N/A Oligonucleotides Sequences of double-strand RNA for RNAi, see Table S3 This Paper N/A Primers for ectopic transgenes construction, see Table S4 This Paper N/A Primers for in situ transgenes construction, see Table S5 This Paper N/A Sequences for sgRNA-mediated gene editing, see Table S6 This Paper N/A Primers for cRT and qRT assays, see Table S7 This Paper N/A Other Selected rRNA processing and ribosome assembly factors tested by RNAi screening, see Table S1 This Paper N/A ..
In Situ:Article Title: rRNA intermediates coordinate the formation of nucleolar vacuoles in C. elegans.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays GoScript Reverse Transcription System Promega Cat#A5000/A50001 SYBR Green Vazyme Cat#Q111-02/03 ClonExpress MultiS One Step Cloning Kit Vazyme Cat#C113-02 T4 RNA ligase I (ssRNA Ligase) BioLabs Cat#M0204SVIAL Actinomycin D MCE Cat#HY-17559 SYTO RNASelect Green Invitrogen Cat#S32703 Experimental models: Organisms/strains C. elegans Strains, see Table S2 This Paper N/A Oligonucleotides Sequences of double-strand RNA for RNAi, see Table S3 This Paper N/A Primers for ectopic transgenes construction, see Table S4 This Paper N/A Primers for in situ transgenes construction, see Table S5 This Paper N/A Sequences for sgRNA-mediated gene editing, see Table S6 This Paper N/A Primers for cRT and qRT assays, see Table S7 This Paper N/A Other Selected rRNA processing and ribosome assembly factors tested by RNAi screening, see Table S1 This Paper N/A ..
Recombinant:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
Transfection:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
Magnetic Beads:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
BIA-KA:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
Modification:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
Staining:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
Imaging:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
Western Blot:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
TUNEL Assay:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
RNA sequencing:Article Title: METTL3 regulates cartilage development and homeostasis by affecting Lats1 mRNA stability in an m 6 A-YTHDF2-dependent manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies METTL3 Rabbit monoclonal antibody Abcam Cat#ab195352; RRID:AB_2721254 YAP1 Rabbit Polyclonal antibody Proteintech Cat#13584-1-AP; RRID:AB_2218915 Phospho-YAP (Ser127) (D9W2I) Rabbit monoclonal antibody Cell Signaling Technology Cat#13008; RRID:AB_2650553 LATS1 Rabbit Polyclonal antibody Proteintech Cat#17049-1-AP; RRID:AB_2281011 YTHDF2 Rabbit Polyclonal antibody Proteintech Cat#24744-1-AP; RRID:AB_2687435 COL2A1 Rabbit Polyclonal antibody Abclonal technology Cat#A19308; RRID: AB_3101745 Collagen X Rabbit monoclonal antibody Abcam Cat#ab49945; RRID:AB_869204 Alpha Tubulin Rabbit Polyclonal antibody Proteintech Cat#11224-1-AP; RRID:AB_2210206 Normal Rabbit IgG Cell Signaling Technology Cat#2729; RRID:AB_1031062 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat#7074; RRID:AB_2099233 Anti-Rabbit IgG H&L (Alexa Fluor 555) Abcam Cat#ab150078; RRID:AB_2722519 Chemicals, peptides, and recombinant proteins Tamoxifen Sigma Cat#T5648 DMEM/F12 medium Gibco Cat#11320033 Fetal bovine serum Gibco Cat#10099141C Penicillin/streptomycin HyClone Cat#SV30010 Lipofectamine RNAiMAX transfection reagent Invitrogen Cat#13778150 TRIzol reagent Invitrogen Cat#15596026 5-ethynyl-20-deoxyuridine (EdU) Sigma Cat#61135-33-9 Actinomycin D MCE Cat#HY-17559 Protein A/G magnetic beads Invitrogen Cat#80104G XMU-MP-1 MCE Cat#HY-100526 ITS-G Gibco Cat#41400045 RNA fragmentation reagents Invitrogen Cat#AM8740 DAPI Solarbio Cat#C0065 Ascorbic Acid Sigma Cat#255564 Critical commercial assays EpiQuik CUT&RUN m6A RNA Enrichment(MeRIP) Kit Epigentek Group Inc. Cat#P-9018 PrimeScriptTM RT reagent Kit with gDNA Eraser Takara Cat#RR047A BCA assay kit Beyotime Cat#P0010 Modified Safranin-O and Fast Green Stain Kit Solarbio Cat#G1371 Poly-HRP goat anti-rabbit IgG kit Boster Biological Technology Cat#SV0002 AEC staining solution kit Boster Biological Technology Cat#AR1020 BD PharmingenTM FITC Annexin V Apoptosis Detection Kit BD Cat#556547 Click-iT Plus EdU Imaging Kits Invitrogen Cat#C10640 Epi-SELECTTM m6A site identification kit Epibiotek Co., Ltd. Cat#R202106M-01 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 DeadEndTM Fluorometric TUNEL System Promega Cat#G3250 Deposited data RNA-Seq data This study GSA: CRA014705 MERIP-Seq data Chelmicki et al.30 GEO: GSE145315 (Continued on next page) 16 Cell Reports 43, 114535, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Mouse:ATDC5 Cells Cobioer Biosciences Co., LTD Cat#CBP60425; RRID: CVCL_3894 Experimental models: Organisms/strains Mouse: B6.Cg-Acantm1(cre/ERT2)Crm/J The Jackson laboratory Strain#019418 Mouse: Mettl3fl/fl Wu et al.21 N/A Oligonucleotides Mouse Mettl3 siRNA Forward: 50-GGCACUUG GAUUUAAGGAATT-30 This paper N/A Mouse Mettl3 siRNA Reverse: 50-UUCCUUAA AUCCAAGUGCCTT-30 This paper N/A Mouse Ythdf2 siRNA Forward: 50-CCAUGAUU GAUGGACAGUCAGCUUU-30 This paper N/A Mouse Ythdf2 siRNA Reverse: 50-AAAGCUGA CUGUCCAUCAAUCAUGG-30 This paper N/A Genotyping primers used in this study This paper See Table S1 RT-qPCR primers used in this study This paper See Table S2 SELECT primers used in this study This paper See Table S3 Software and algorithms ImageJ Version 1.53 NIH Image https://imagej.net/ Prism Version 10.1.0 GraphPad Software http://graphpad.com/ R version 4.2.2 The Comprehensive R Archive Network https://cran.r-project.org/ FastQC The Babraham Bioinformatics group https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ DESeq2 Love et al.55 https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html ClusterProfiler Yu et al.56 https://bioconductor.org/ packages/release/bioc/html/ clusterProfiler.html Hisat2 Kim et al.54 https://daehwankimlab.github.io/ hisat2/ GSEA Version 4.3.2 Subramanian et al.57 https://www.gsea-msigdb.org/ SRAMP Zhou et al.60 http://www.cuilab.cn/sramp/ NovoExpress Version 1.6.2 Agilent Technologies, Inc. https://www.agilent.com/en/ product/research-flow-cytometry/ flow-cytometry-software/novocytenovoexpress-software-1320805 Integrative Genome Viewer Version 2.4.9 The IGV Team https://www.igv.org/
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