Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-PCM1 (dilution 1:100) | Sigma Aldrich | Cat# HPA023370 |
| AF647 Rabbit anti-Laminin (dilution 1:200) | Novus biologicals | Cat# NB300-144AF647 |
| AF750 Rabbit anti-Laminin (dilution 1:100) | Novus biologicals | Cat# NB300-144AF750 |
| Rabbit anti-Ki67 (dilution 1:100) | Abcam | Cat# ab15580 |
| Mouse anti-SV2 (dilution 1:200) | DSHB | Cat# AB_2315387 |
| Mouse anti-2H3 (NF) (dilution 1:200) | DSHB | Cat# AB_531793 |
| AF488 Goat anti-Rabbit (dilution 1:300) | ThermoFisher Scientific | Cat# A-11008 |
| AF568 Goat anti-Rabbit (dilution 1:300) | ThermoFisher Scientific | Cat# A-11036 |
| AF647 Goat anti-Rabbit (dilution 1:300) | ThermoFisher Scientific | Cat# A-21245 |
| AF647 Goat anti-Mouse (dilution 1:300) | ThermoFisher Scientific | Cat# A-21235 |
| AF750 Goat anti-Mouse (dilution 1:100) | ThermoFisher Scientific | Cat# A-21037 |
| PE-Cy7-conjugated anti-CD45 (dilution 1:200) | Biolegend | Cat# 103114 |
| PE-Cy7-conjugated anti-Sca1 (dilution 1:200) | Biolegend | Cat# 108114 |
| BV605-conjugated anti-CD31 (dilution 1:200) | Biolegend | Cat# 102427 |
| Biological samples | ||
| Denervated human muscle biopsies | Hospital Clinic (Barcelona, Spain) | N/A |
| Exercised human muscle biopsies | University of Valencia | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Biotin-conjugated a-bungarotoxin (dilution 1:100) | Alomone Labs | Cat# B-100-B |
| AF488-conjugated a-bungarotoxin (dilution 1:100) | Biotium | Cat# 00005 |
| AF488 Streptavidin (dilution 1:200) | ThermoFisher Scientific | Cat# S32354 |
| AF594 Streptavidin (dilution 1:200) | ThermoFisher Scientific | Cat# S32356 |
| AF647 Streptavidin (dilution 1:200) | ThermoFisher Scientific | Cat# S32357 |
| DAPI (dilution 1:500) | ThermoFisher Scientific | Cat# 62248 |
| Topro3 (dilution 1:10000) | Invitrogen | Cat# T3605 |
| Urea | Sigma Aldrich | Cat# 51456 |
| Quadrol | Sigma Aldrich | Cat# 122262 |
| Triton-X100 | Sigma Aldrich | Cat# T8787 |
| Triethanolamine (TEA) | Sigma Aldrich | Cat# 90278 |
| Sucrose | Sigma Aldrich | Cat# S0389 |
| Ethynyl-deoxyuridine (EdU) | Invitrogen | Cat# A10044 |
| 4% Paraformaldehyde (PFA) | Cole-Parmer | Cat# CF100400-1A |
| Bobine Serum Albumin (BSA) | Sigma Aldrich | Cat# A7030 |
| M.O.M. blocking solution | Vector Laboratories | Cat# MKB-2213-1 |
| Liberase | Roche | Cat# 5401020001 |
| Dispase | Sigma Aldrich | Cat# D4693 |
| Fetal bobine serum (FBS) | Gibco | Cat# 26-170-043 |
| UltraPure BSA | ThermoFisher Scientific | Cat# AM2616 |
| Hematoxylin | Sigma Aldrich | Cat# MH16 |
| Eosin | Sigma Aldrich | Cat# HT110216 |
| TRIzol | ThermoFisher Scientific | Cat# 15596026 |
| Opal 570 | Akoya Biosystems | SKU FP1488001KT |
| Opal 690 | Akoya Biosystems | SKU FP1497001KT |
| Wheat germ agglutinin (WGA) | Biotium | Cat# 29077 |
| Critical commercial assays | ||
| RNAscope Multiplex Fluorescent Reagent Kit v2 | ACD Bio-Techne | Cat# 323270 |
| Click-IT EdU Cell Proliferation Kit for Imaging, Alexa Fluor 488 dye | ThermoFisher Scientific | Cat# C10337 |
| RNeasy Mini Kit (50) | Qiagen | Cat# 74104 |
| Chromium Nuclei Isolation Kit | 10X Genomics | Cat# 1000494 |
| Qubit 1X dsDNA High Sensitivity (HS) Assay Kits | ThermoFisher Scientific | Cat# Q33231 |
| Single Cell 3′ Reagent Kit v3.1 (dual index) | 10X Genomics | Cat# PN-1000268 |
| NEBNext Ultra™ II RNA Library Prep Kit for Illumina | NEB | Cat# E7775 |
| Visium Spatial Tissue Optimization Slide & Reagent Kit | 10X Genomics | Cat# PN-1000193 |
| NEBNext Poly(A) mRNA Magnetic Isolation Module | NEB | Cat# E7490 |
| Ultra II Directional RNA Library Prep Kit for Illumina | NEB | Cat# E7760 |
| Watchmaker mRNA Library Prep Kit v1.1.0823 | Watchmaker Genomics | Cat# 7BK0001 |
| SMART-Seq mRNA LP kit | Takara Bio | Cat# 634768 |
| Deposited data | ||
| scRNA-seq, snRNA-seq, bulk RNA-seq and spatial transcriptomics | This paper | GSE294765, GSE311567 and GSE312393 |
| scRNA-seq data from Schwann cells in denervated muscles at different time points | Nicoletti et al.22 | GSE221736 |
| Microarray data from human muscles with spinal cord injury | Urso et al.42 | GSE21496 and GSE21497 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | Charles River Laboratories | https://www.criver.com/products-services/find-model/c57bl6-mouse?region=3611 |
| Mouse: Plp1-CreER | The Jackson Laboratory | Cat# 005975 |
| Mouse: Rosa26-LSL-tdTomato | The Jackson Laboratory | Cat# 007909 |
| Oligonucleotides | ||
| Cell Multiplexing Oligos (CMOs) | 10X Genomics | https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/sequencing/cell-multiplexing-oligo-sequences-cell-ranger |
| Inhba-C2 | ACD Bio-Techne | Cat# 455871-C2 |
| Ajap1-C3 | ACD Bio-Techne | Cat# 549641-C3 |
| Col20a1-C1 | ACD Bio-Techne | Cat# 455771 |
| INHBA-C2 | ACD Bio-Techne | Cat# 415111-C2 |
| CHRNE-C3 | ACD Bio-Techne | Cat# 1242771-C1 |
| Software and algorithms | ||
| Fiji | Open platform | https://fiji.sc/ |
| BioRender | Web based | https://www.biorender.com/ |
| GraphPad Prism 10 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| CellChat (v2.1.2) | Jin et al.31 | http://www.cellchat.org/ |
| Cell Ranger (v7.1.0) | 10X Genomics | https://www.10xgenomics.com/support/software/cell-ranger/downloads/previous-versions |
| MyoSight | Babcock et al.50 | https://github.com/LyleBabcock/MyoSight/tree/master |
| Dropkick (v1.2.7) | Heiser et al.51 | https://pypi.org/project/dropkick |
| Solo (v1.3) | Bernstein et al.52 | https://github.com/calico/solo |
| Seurat (v5.0.1) | Hao et al.53 | http://www.satijalab.org/seurat |
| SoupX | Young and Behjati54 | https://github.com/constantAmateur/SoupX |
| Harmony (v1.2.0) | Korsunsky et al.55 | https://github.com/immunogenomics/harmony |
| SpaceRanger (v2.0.0) | 10X Genomics | https://www.10xgenomics.com/support/software/space-ranger/downloads/previous-versions |