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    Bio-Rad algorithms prism 10 software graphpad software imagej nih
    Algorithms Prism 10 Software Graphpad Software Imagej Nih, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 36323 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/algorithms+prism+10+software+graphpad+software+imagej+nih/Image+Lab+Software/pm40768332-274-64-84
    Average 99 stars, based on 36323 article reviews
    algorithms prism 10 software graphpad software imagej nih - by Bioz Stars, 2026-09
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    Related Articles

    Quantitative RT-PCR:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Negative Control:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Recombinant:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Software:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    RNA Sequencing:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Sequencing:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Metabolomic:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Targeted Proteomics:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Mass Spectrometry:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Real-time Polymerase Chain Reaction:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..

    Imaging:

    Article Title: Multi-dimensional metabolomic remodeling under diverse muscle atrophic stimuli in vivo.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TSKgel Amide-80 (3.0 μm, 2.0 mm × 15 cm TOSOH Corporation Cat# 0021865 G266 DNA Damage Detection Kit - γH2AX - Red Dojindo Molecular Technologies Cat# 340-09431 HEPES Nacalai Tesque Cat# 02443-34 Trichloroacetic acid Nacalai Tesque Cat# 06275-24 L-Methionine sulfome Thermo Fisher Cat# A17027 Takara Taq Takara Cat# R001A Takara Ex Taq Takara Cat# RR001A Agarose for ≧1kbp fragment (Fine Powder) Nacalai Tesque Cat# 02468-95 100 bp DNA ladder One Nacalai Tesque Cat# 07908-75 6x Loading Dye Toyobo Cat# RE-DYE Ethidium Bromide Solution Nacalai Tesque Cat# 14631-94 Sodium Chloride Nacalai Tesque Cat# 31320-05 Bacto TM Peptone DIFCO Cat# 0118-17-0 Extract Yeast Dried Nacalai Tesque Cat# 15838-45 Bacto TM Agar BD Cat# 214010 Competent Quick DH5α Toyobo Cat# DNA-913 Ampicillin Sodium Salt Nacalai Tesque Cat# 02739-74 KOD-Plus-Neo Toyobo Cat# KOD-401 QIAGEN Plasmid Midi kit QIAGEN Cat# 12145 Calf intestine alkarine phosphatase Takara Cat# 2250A QIAEX II Gel Extraction Kit QIAGEN Cat# 20021 DNA Ligation Kit Ver.2.1 Takara Cat# 6022 Venoject II Terumo Cat# VP-DK051K Isoflurane Viatris – Domitor Nippon Zenyaku Kogyo – Midazolam Sandoz – Vetorphale Meiji Seika Pharma – Antisedan Nippon Zenyaku Kogyo – Deposited data Metabolomics data (Skeletal muscle, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003721; Project ID: PR002310 Metabolomics data (plasma, FoxO1 overexpression and immobilization, FoxO1-Tg and C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003722; Project ID: PR002311 Metabolomics data (Skeletal muscle, Cancer cachexia and starvation, C57BL/6J) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003723; Project ID: PR002312 Metabolomics data (Skeletal muscle, immobilization, mFoxO1,3,4 flox/flox and mFoxO1,3,4 − /− ) https://www. metabolomicsworkbench.org Metabolomics Workbench Study ID: ST003724; Project ID: PR002313 Experimental models: Cell lines LLC cells: LL/2 (LLC1) ATCC CRL-1642 Primary myoblast This paper N/A C2C12 myoblasts Riken Cell Bank RCB0987 C2C12 myoblasts (Western blot analysis for SUnSET analysis and MG-132 experiment) ATCC CRL-1772 HEK293T cells Oyabu et al. 29 N/A Experimental models: Organisms/strains Mouse: C57BL/6J CLEA – Mouse: HSA-FOXO1-Tg Kamei Lab N/A Mouse: HSA-Cre FoxO1,3,4 flox/flox Kamei Lab N/A Mouse: HSA-DN-FOXO1-Tg Yamazaki et al. 42 N/A (Continued on next page) Cell Reports 44, 116097, August 26, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for genotyping This paper Table S1 Primer for RT-qPCR This paper Table S2 MISSION siRNA Universal Negative Control #1 Sigma-Aldrich Cat# SIC001 MISSION siAmd2_1 Sigma-Aldrich Cat# SASI_Mm02_00311615 MISSION siAmd2_2 Sigma-Aldrich Cat# SASI_Mm01_00156378 Recombinant DNA pCAG-FOXO1(3A) Oyabu et al. 29 N/A pCMX-GFP Oyabu et al. 29 N/A pGL3-Odc1 promoter-luciferase This paper N/A phRL-TK Promega Cat# E2241 Software and algorithms Prism 10 software GraphPad Software – ImageJ NIH https://imagej.nih.gov/ij/download.html BZ-X800 Viewer Keyence – BZ-X800 Analyzer Keyence – ImageLab software Bio-Rad – Venn Diagrams Bioinformatics & Evolutionary Genomics http://bioinformatics.psb.ugent.be/ webtools/Venn/ Cluster 3.0 de Hoon et al. 43 http://bonsai.hgc.jp/∼mdehoon/ software/cluster/ Java TreeView Saldanha et al. 44 https://jtreeview.sourceforge.net MasterHands ver.2 software (Keio University, Tsuruoka, Yamagata, Japan) Sugimoto t al. 45 N/A MetaboAnalyst Pang et al. 46 https://www.metaboanalyst.ca/ LabSolutions LCMS Shimadzu N/A RNAseqChef Etoh and Nakao 47 https://imeg-ku.shinyapps.io/RNAseqChef/ GREIN: GEO RNA-seq Experiments Interactive Navigator Mahi et al. 48 https://www.ilincs.org/apps/grein/ SarcoAtlas Ham et al. 49 and Borsch et al. 50 https://sarcoatlas.scicore.unibas.ch Ensembl Harrison et al. 51 https://asia.ensembl.org Clustal Omega Multiple sequence Alighment (MSA) Madeira et al. 52 https://www.ebi.ac.uk/ jdispatcher/msa/clustalo R system R Core Team https://cran.r-project.org Programming environment of R: RStudio RStudio Team https://www.rstudio.com Adobe Illustrator Adobe https://www.adobe.com Excel Microsoft https://www.microsoft.com/ en-us/microsoft-365/excel BioRender: Scientific Image and Illustration Software N/A https://www.biorender.com Primer Express 2.0 Thermo Fisher – Primer-BLAST NIH https://www.ncbi.nlm.nih.gov/tools/primer- blast/https://www.ilincs.org/apps/grein/ Other Metabolomic analyses (CE-TOFMS) Human Metabolome Technologies N/A Agilent CE-TOFMS system Agilent Technologies – LCMS-8040 triple quadrupole mass spectrometer Shimadzu – Grip strength meter Melquest Cat# GPM-101B CFX Connect Real-Time PCR Detection System Bio-Rad Cat# 1855201J1 ChemiDoc XRS+ Imaging System Bio-Rad Cat# 1708265J1 (Continued on next page) 20 Cell Reports 44, 116097, August 26, 2025 ..



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