Voluntary wheel running improves molecular and functional deficits in a murine model of facioscapulohumeral muscular dystrophy

. 2023 Dec 2;27(1):108632. doi: 10.1016/j.isci.2023.108632

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Rat monoclonal (rat IgG1 isotype) Anti-Laminin-2 (alpha-2 Chain) antibody - clone 4H8-2	Sigma-Aldrich	Cat# L0663; RRID: AB_477153
Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 488	Invitrogen	Cat# A32766; RRID: AB_2866493
Mouse Myosin heavy chain, Type IIX Monoclonal (MIgM)	Developmental Studies Hybridoma Bank	Cat# 6H1; RRID: AB_1157897
Mouse Myosin heavy chain Type IIA Monoclonal (MIgG1)	Developmental Studies Hybridoma Bank	Cat# SC-71; RRID: AB_2147165
Mouse Myosin heavy chain Type I Monoclonal (MIgG2b)	Developmental Studies Hybridoma Bank	Cat# BA-D5; RRID: AB_2235587
Rabbit polyclonal antibody to Dystrophin (IgG)	Abcam	Cat# ab15277; RRID: AB_301813
Goat anti-Mouse Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody 405	Invitrogen	Cat# A-31553; RRID: AB_221604
Goat anti-Mouse IgG1 Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 488	Invitrogen	Cat# A-21121; RRID: AB_2535764
Goat Anti-Mouse IgM Antibody, μ chain, Cy3 conjugate	Millipore Sigma	Cat# AP128C; RRID: AB_92478
Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 647	ThermoFisher	Cat# A-21245; RRID: AB_2535813

Biological samples

Mouse Skeletal Muscles (triceps, FDB)	This Study	N/A

Chemicals, peptides, and recombinant proteins

Hoescht 33342 dye	Abcam	Cat# ab228551
Epredia™ Shandon™ Bluing Reagent	Epredia™	Cat# 6769001
Epredia™ Richard-Allan Scientific™ Eosin-Y Alcoholic	Epredia™	Cat# 71204
Epredia™ Signature Series™ Hematoxylin 7211	Epredia™	Cat# 7211
Epredia™ Signature Series™ Clarifier™ 1	Epredia™	Cat# 7441
Fisher Chemical™ Permount™ Mounting Medium	FisherScientific	Cat# SP15-100
Xylenes (CAS 1330-20-7)	Sigma-Aldrich	Cat# 214736
Epredia™ Dehydrant Alcohol 100%	Epredia™	Cat# 6201
Epredia™ Dehydrant Alcohol 100%	Epredia™	Cat# 6301
Bovine Serum Albumin (CAS 9048-46-8)	Sigma-Aldrich	Cat# A3294-500G
Normal Goat Serum	Vector Laboratories	Cat# S-1000-20
Gibco Horse Serum, heat inactivated, New Zealand origin	ThermoFisher	Cat# 26050088
M.O.M blocking reagent	Vector Laboratories	Cat# MKB-2213-1
Gibco PBS, pH 7.4	ThermoFisher	Cat# 10010023
ProLong Gold Antifade Mountant	Invitrogen	Cat# P36930
Collagenase, Type II, powder	ThermoFisher	Cat# 17101015
Gibco Penicillin-Streptomycin (5,000 U/mL)	ThermoFisher	Cat# 15070063
Gibco DMEM, high glucose, pyruvate	ThermoFisher	Cat# 11995065
Gibco Sodium Pyruvate (100 mM)	ThermoFisher	Cat# 11360070
Gibco Sodium Bicarbonate 7.5% solution	ThermoFisher	Cat# 25080094
Matrigel Matrix	Corning Inc.	Cat# 356234
Sodium Chloride (NaCl) (CAS 7647-14-5)	Sigma-Aldrich	Cat# S9888-25G
Ethylenediaminetetraacetic acid (EDTA) (CAS 60-00-4)	Sigma-Aldrich	Cat# E9884
Sodium dodecyl sulfate (SDS) (CAS 151-21-3)	Sigma-Aldrich	Cat# 436143
TRIS hydrochloride (Tris-HCl) (CAS 1185-53-1)	Sigma-Aldrich	Cat# 10812846001
Proteinase K, recombinant, PCR grade	ThermoFisher	Cat# EO0491
Fetal Bovine Serum, Premium	Bio-Techne	Cat# S11150
HEPES (CAS 7365-45-9)	Sigma-Aldrich	Cat# 54457
Hanks Balanced Salts Solution	Sigma-Aldrich	Cat# H9269
FM1-43 dye ((N-(3-Triethylammoniumpropyl)-4-(4-(Dibutylamino) Styryl) Pyridinium Dibromide)	ThermoFisher	Cat# T3163
Calcium Chloride (CaCl₂) (CAS 10043-52-4)	Sigma-Aldrich	Cat# C4901
Trichrome Stain Kit (Connective Tissue Stain)	Abcam	Cat# ab150686

Critical commercial assays

Agilent Fragment Analyzer high-sensitivity assay	Agilent	Cat# DNF-472-1000
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina	Lexogen	N/A
Seahorse XFe24 Mito Stress Test Kit	Agilent	Cat# 103015-100
SuperScript™ IV Reverse Transcriptase	Invitrogen	Cat# 18090010
Oligo(dT)12-18 Primer	Invitrogen	Cat# 18418012
SYBR Green Master Mix	Applied Biosystems	Cat# 4309155
GoTaq Green Master Mix	Promega	Cat# M712
100 uM dNTPs	Invitrogen	Cat# 18427013
GoTaq polymerase	Promega	Cat# M3001
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina	Lexogen	N/A
NextSeq 500 v2 High Output SR 75 Cycle	Illumina	N/A

Deposited data

RNA sequencing of mouse triceps brachii muscles	NCBI Gene Expression Omnibus (GEO) database	GSE233340

Experimental models: Organisms/strains

Male and female heterozygous FLExDUX4 mice: B6(Cg)-Gt(ROSA)26Sortm1.1(DUX4∗)Plj/J	Peter & Takako Jones Laboratory (University of Nevada, Reno)	N/A
Male and female wild type (WT) mice: C57BL/6	Peter & Takako Jones Laboratory (University of Nevada, Reno)	N/A

Oligonucleotides

Primers for RT-qPCR, see Table S7	This Paper	N/A
Genotyping PCR Primers, see Table S7	Peter & Takako Jones Laboratory (University of Nevada, Reno)	N/A

Software and algorithms

cutadapt v1.16	Martin M. (2011)⁸¹	https://doi.org/10.14806/ej.17.1.200
FastQC v0.11.7	Andrews S. (2018)⁸²	Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
STAR version 2.5.3a	Dobin et al. (2013)⁸³	https://doi.org/10.1093/bioinformatics/bts635
featureCounts 1.6.2 from Subread package	Liao et al. (2013)⁸⁴	https://subread.sourceforge.net
DESeq2	Love et al. (2014)⁸⁵	https://doi.org/10.1186/s13059-014-0550-8
Gene set enrichment analysis (GSEA v4.1.0)	Subramanian et al. (2005)⁸⁶	https://www.gsea-msigdb.org/gsea/index.jsp
Ingenuity Pathway Analysis (IPA	Qiagen	N/A
GraphPad Prism 8	GraphPad	https://www.graphpad.com/
Cell Profiler	Laghi et al. (2022)⁸⁷	https://cellprofiler.org/
VitalView Software	STARR Life Sciences	https://www.starrlifesciences.com/activity/activity-software/
Parse-Running-Wheel	Uapinyoying (2018)⁸⁸	https://zenodo.org/doi/10.5281/zenodo.10210699
Python	Python.org	N/A

Other

Borosilicate glass bottom chamber slides	ThermoFisher	Cat# 154461