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Charles River Laboratories mouse cd 1 igs
Mouse Cd 1 Igs, supplied by Charles River Laboratories, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cd-1+igs+mouse/balb+c+mice/pmc11652221-586-0-4
Average 86 stars, based on 1 article reviews
mouse cd 1 igs - by Bioz Stars, 2026-10
86/100 stars

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Virus:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

shRNA:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Control:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Recombinant:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Staining:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

RNA Sequencing:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Software:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Saline:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Imaging:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Affinity Purification:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Bicinchoninic Acid Protein Assay:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Western Blot:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Electron Microscopy:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

RNAscope:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Multiplex Assay:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Mass Spectrometry:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Mutagenesis:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Microscopy:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Plasmid Preparation:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.

Mouse Assay:

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GluR1 (mouse) (dilution: 1:250) Novus Biologicals NBP2_22399 Anti-LAMP1 (rabbit) (dilution: 1:500) Abcam Ab24170 Anti-GFP (mouse) (dilution: 1:500) Rockland 600-301-215M Anti-mouse Abberior STAR Orange (dilution: 1:300) Fisher Scientific NC1933863 Anti-rabbit Abberior STAR Red (dilution: 1:1000) Fisher Scientific NC1933870 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 103 Boston BioProducts BM-220, 70011044 Paraformaldehyde (PFA) Sigma-Aldrich 158127-500 g Sucrose Bio Basic SB0498-25 Donkey serum Sigma-Aldrich S30-100 mL Triton X-100 Sigma-Aldrich 9036-19-5 ProLong Diamond antifade mountant Thermo Fisher Scientific P36961 Sodium pentobarbital Vortech Pharmaceuticals 07-894-1075 Scigen Tissue-Plus O.C.T. compound Fisher Healthcare 27-730-571 Sodium azide Sigma-Aldrich S2002-100 g Critical commercial assays ZymoPURE II Zymo Research D4208T Experimental models: Organisms/strains CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) Charles River Strain code 022 Recombinant DNA EGFP under the CAG promoter Addgene Plasmid #11150 Software and algorithms Imspector Abberior Instruments GmbH Imspector Image Acquisition & Analysis Software v16.3 https://imspector.abberior-instruments.com/ ImageJ software (Fiji) Schneider et al., 2012 https://imagej.nih.gov/ij/ (Continued on next page) 8 STAR Protocols 4, 102707, December 15, 2023 Continued REAGENT or RESOURCE SOURCE IDENTIFIER MATLAB MathWorks RRID: SCR_001622 Imaris 9.7 or higher Oxford Instruments RRID: SCR_007370 Spots close to filament border Imaris XTension Imaris Open https://imaris.oxinst.com/open/ Colocalize spots Imaris XTension Imaris Open https://imaris.oxinst.com/open/ GitHub README file GitHub https://github.com/CruzMartinLab/ IMARIS_compiler Other Sliding microtome Leica SM2000 Peristaltic pump Masterflex C/L dual-channel tubing pump Cole Parmer Inverted laser scanning confocal microscope (Nikon Ti2 with perfect focus, P736 Piezo Z-stage with an Abberior Facility Line STED system controlled with the Abberior Imspector software platform) Nikon Instruments, Abberior GmbH, and Physik Instrumente N/A Plan apochromat 60 3 1.4 NA oil immersion objective Nikon Instruments N/A 1 mm coverslips Corning 2975-225 ll OPEN ACCESSProtocol

Article Title: A pipeline for STED super-resolution imaging and Imaris analysis of nanoscale synapse organization in mouse cortical brain slices
Article Snippet: CD-1 IGS mouse (wild type, postnatal day (P) 18–25, male and female mice) , Charles River , Strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Briefly, unilateral, global (C5–T1), post- ganglionic NBPIs were surgically created in P5 wildtype female and male mice (Charles River; CD- 1 IGS mouse, strain code 022) by extraforaminal nerve root excision under isoflurane anesthesia.

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina
Article Snippet: Mus musculus : CD-1 IGS mouse , Charles River , Strain Code: 022 RRID:IMSR_CRL:022.

Article Title: Clonally heritable gene expression imparts a layer of diversity within cell types.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Peptide: LLWNGPMAV (HLA-A2/YFV NS4B) JPT Peptide Technologies Cat#SP-MHCI-0063 Agencourt Ampure XP Beads BeckmanCoulter Cat#A63881 EDTA (0.5M) ThermoFisher Cat#AM9261 Sodium Dodecyl sulfate 20% ThermoFisher Cat#AM9820 TE Buffer (pH 8.0) RNAse Free ThermoFisher Cat#AM9849 Critical commercial assays Agilent High Sensitivity Kit Agilent Technologies Cat#5067-4626 QuantiFluor dsDNA System Promega Cat#E2670 CD8 T cell Negative Selection Kit (Human) Miltenyi Biotec Cat#130-096-495 GenomePlex Single Cell WGA4 kit Sigma-Aldrich Cat#WGA4-50RXN Deposited data Supplemental Tables are on Zenodo This Paper https://zenodo.org/records/10407870 Mouse cortex, processed data are deposited on GEO server This Paper https://www.ncbi.nlm.nih.gov/geo/ query/acc.cgi?acc=GSE252510 Sensitive raw human data are deposited on a secure server European Genome-Phenome Archive (EGA) under accession number EGA50000000154 and can be accessed via application to EGA This Paper https://ega-archive.org/ Experimental models: Organisms/strains CD-1 IGS Mouse Charles River (Germany) Crl:CD1(ICR) Oligonucleotides /5Biosg/ACGAGCATCAGCAGCA TACGATTTTTTTTTTTTTTTTTT TTTTTTTTTTTTVN Smartseq3_ OligodT30VN IDT /5Biosg/AGAGACAGATTGCGC AATGNNNNNNNNrGrGrG Smartseq3_N8_TSO IDT

Article Title: The role of sympathetic innervation in neonatal muscle growth and neuromuscular contractures.
Article Snippet: The following two species were used in this study: wild-type mice (Charles River; CD-1 IGS mouse, strain code 022), and wild-type rats (Charles River; Sprague–Dawley rat, strain code 400).

Article Title: Selenoprotein P is a target for regulating extracellular vesicle biogenesis and secretion from activated microglia in vivo
Article Snippet: Mouse: CD-1 ® IGS Mouse , Charles River Laboratories , strain code 022.

Article Title: Sex-specific role of myostatin signaling in neonatal muscle growth, denervation atrophy, and neuromuscular contractures
Article Snippet: Biological sample (CD-1 IGS mouse) , Mouse , Charles River , , Strain code 022.



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Charles River Laboratories cd-1® igs mouse [crl:cd1(icr)]
Cd 1® Igs Mouse [Crl:Cd1(icr)], supplied by Charles River Laboratories, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cd-1+igs+mouse/c57bl+6+mice/10__1016_slash_j__isci__2025__113076-327-15-21
Average 90 stars, based on 1 article reviews
cd-1® igs mouse [crl:cd1(icr)] - by Bioz Stars, 2026-10
90/100 stars
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90
Charles River Laboratories cd-1® igs mouse (strain 022)
Cd 1® Igs Mouse (Strain 022), supplied by Charles River Laboratories, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cd-1+igs+mouse/c57bl+6+mice/bio_rxiv__2025__06__26__661592-42-2-11
Average 90 stars, based on 1 article reviews
cd-1® igs mouse (strain 022) - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier

90
Charles River Laboratories cd-1® igs mouse
Cd 1® Igs Mouse, supplied by Charles River Laboratories, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cd-1+igs+mouse/c57bl+6+mice/pmc12208326-14-0-5
Average 90 stars, based on 1 article reviews
cd-1® igs mouse - by Bioz Stars, 2026-10
90/100 stars
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90
Charles River Laboratories mouse: cd-1 igs
Mouse: Cd 1 Igs, supplied by Charles River Laboratories, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cd-1+igs+mouse/cd+1+igs++outbred+stock++mice/pm40347943-872-68-73
Average 90 stars, based on 1 article reviews
mouse: cd-1 igs - by Bioz Stars, 2026-10
90/100 stars
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96
Proteintech mouse anti cd 206
Mouse Anti Cd 206, supplied by Proteintech, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cd-1+igs+mouse/CD206+Antibody/pm39946768-87-35-39
Average 96 stars, based on 1 article reviews
mouse anti cd 206 - by Bioz Stars, 2026-10
96/100 stars
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96
Proteintech monoclonal mouse anti bovine cd 63 antibody
Monoclonal Mouse Anti Bovine Cd 63 Antibody, supplied by Proteintech, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cd-1+igs+mouse/CD63+Antibody/pm39892598-122-19-47
Average 96 stars, based on 1 article reviews
monoclonal mouse anti bovine cd 63 antibody - by Bioz Stars, 2026-10
96/100 stars
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