KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-mouse Thrombospondin-1 (clone A6.1) | eBioscience | Cat# 14-9756-82 |
| anti-mouse α7 integrin (clone 3C12) | MBL international | Cat# K0046-3 |
| anti-mouse CD29 (clone 9EG7) | BD Biosciences | Cat# 553715 |
| anti-mouse CXCR4 (clone 2B11) | BD Biosciences | Cat# 551852 |
| anti-mouse CD31 (clone MEC 13.3) | BD Biosciences | Cat# 550274 |
| anti-mouse CD45 (clone 30-F11) | BD Biosciences | Cat# 553076 |
| anti-mouse CD11b (clone M1/70) | BD Pharmigen | Cat# 557394 |
| anti-mouse Sca-1 (clone E13-161.7) | BD Biosciences | Cat# 553333 |
| anti-mouse CD106 (clone MVCAM.A) | Biolegend | Cat# 105701 |
| anti-mouse CD9 (clone KMC8) | eBiosciences | Cat# 14-0091-82 |
| anti-mouse CD44 (clone IM-7) | BD Biosciences | Cat# 553131 |
| anti-mouse CD47 (clone MIAP301) | Biolegend | Cat# 127502 |
| Rat IgG2a, k | Biolegend | Cat# 400502 |
| anti-Rat IgG2a PerCP-eFluor 710 | eBioscience | Cat# 46-4817-82 |
| anti-mouse CD90.2 (clone 30-H12) | BD Biosciences | Cat# 553009 |
| anti-mouse CD98 (clone 4F2) | Biolegend | Cat# 128202 |
| anti-mouse CD104 (clone 346-11A) | BD Biosciences | Cat# 553745 |
| anti-mouse Pax7 (clone PAX7) | Santa Cruz Biotechnology | Cat# sc-81648 |
| anti-mouse Myf5 (clone C-20) | Santa Cruz Biotechnology | Cat# sc-302 |
| anti-mouse MyoD (clone 5.8A) | BD Pharmigen | Cat# 554130 |
| anti-mouse Myogenin (clone F5D) | BD Pharmigen | Cat# 556358 |
| anti-pRb-166Er | Fluidigm | Cat# 3166011A |
| anti-Mouse CD45 (30-F11)-89Y | Fluidigm | Cat# 3089005B |
| anti-Mouse CD11b (M1/70) -148Nd | Fluidigm | Cat# 3148003B |
| anti-human/mouse CD44-Yb171 | Fluidigm | Cat# 3171003B |
| anti-Laminin | Abcam | Cat# ab11575 |
| anti-eMHC (clone F1.562) | DSHB | N/A |
| Biotin anti-mouse CD11b (Clone M1/70) | BD Biosciences | Cat# 553309 |
| Biotin anti-mouse CD45 (Clone 30F11) | BD Biosciences | Cat# 553078 |
| Biotin anti-mouse Sca1 (Clone E13-161.7) | BD Biosciences | Cat# 553334 |
| Biotin anti-mouse CD31 (Clone 390) | eBioscience | Cat# 13-0311-82 |
| anti α7integrin-PE (clone R2F2) | AbLab | Cat# 10ST215 |
| anti-CD34-eFluor660 (clone RAM34) | eBioscience | Cat# 50-0341-82 |
| Streptavidin APC-Cy7 | BD Biosciences | Cat# 554063 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 16% Paraformaldehyde aqueous solution (PFA) | Electron Microscopy Sciences | Cat# 15711 |
| 4’,6 diamidino-2-phenylindole (DAPI) | Life Technologies | Cat# D1306 |
| D-Luciferin | Caliper Life Sciences | Cat# 122796 |
| Collagenase type 2 | Worthington | Cat# LS004176 |
| Dispase II | Thermo Fisher Scientific | Cat# 17105041 |
| Tamoxifen | VWR | Cat# AAJ63509-03 |
| Dimethyl Sulfoxide (DMSO) | Sigma | Cat# D8418 |
| Notexin | Latoxan | Cat# L8104 |
| Cisplatin | Sigma-Aldrich | Cat# P4394 |
| Cell-ID intercalator-Ir | Fluidigm | Cat# 201192B |
| 5-Iodo-2′-deoxyuridine | Sigma Aldrich | Cat# I7125 |
| Perm/Wash Buffer I | BD Biosciences | Cat# 557885 |
| Endoporter-PEG | Gene Tools | Cat# OT-EP-PEG-1 |
| DMEM, low glucose, pyruvate | Thermo Fisher Scientific | Cat# 11885-092 |
| Ham’s F-10 Nutrient Mix | Invitrogen | Cat# 11550-043 |
| Horse Serum | Fisher-Scientific | Cat# 26-050-088 |
| Penicillin/Streptomycin | Gibco | Cat# 15140122 |
| Recombinant Human FGF-basic | Peprotech | Cat# 100-18B |
| Critical Commercial Assays | ||
| PrimeFlow RNA Assay Kit | Thermo Fisher Scientific | Cat# 88-18005-204 |
| Custom Probe-CD47long 3’UTR | Thermo Fisher Scientific | Assay ID: VB6-6001206 |
| Custom Probe-CD47total | Thermo Fisher Scientific | Assay ID: VB1-3030381 |
| RNeasy Micro Kit | Qiagen | Cat# 74004 |
| High-Capacity cDNA reverse transcription kit | Applied Biosystems | Cat# 4368814 |
| TaqMan gene expression Master Mix | Applied Biosystems | Cat# 4370048 |
| SYBR Green PCR Master Mix | Life Technologies | Cat# 4309155 |
| Green Down cADDis cAMP Assay Kit | Montana Molecular | Cat# D0200G |
| Cyclic AMP XP Assay Kit | Cell Signaling Technology | Cat# 4339 |
| Ovation RNA-Seq System V2 kit | NuGen | Cat# 7102-08 |
| TruSEQ RNA Library Preparation Kit v2 | Illumina | Cat# RS-122-2101 |
| Nextera DNA Library Prep Kit | Illumina | Cat# FC-121-1030 |
| Deposited Data | ||
| RNAseq data | This study | GSE198249 |
| CyTOF Data | This study | FR-FCM-Z5RA, FR-FCM-Z5RB, FR-FCM-Z5RC, FR-FCM-Z5RD, FR-FCM-Z5RE, FR-FCM-Z5RG, FR-FCM-Z5RF |
| Experimental Models: Cell Lines | ||
| Primary Myoblasts | In house | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | Jackson Laboratories | Strain# 000664 |
| Mouse: Pax7tm1(cre/ERT2)Gaka (Pax7Cre-ERT2) | Jackson Laboratories | Strain# 017763 |
| Mouse: Gt(ROSA)26Sortm1(Luc)Kael (Rosa26LSL-Luc) | Jackson Laboratories | Strain# 005125 |
| Mouse: B6.129S7-Cd47tm1Fpl/J | Jackson Laboratories | Strain# 003173 |
| Mouse: NOD.Cg-Prkdcscid/J | Jackson Laboratories | Strain# 001303 |
| Oligonucleotides | ||
| q-RT-PCR Primer Sequences | Integrated DNA Technologies | Table S1 |
| Antisense Morpholino Oligonucleotides Sequences | Gene Tools | Table S2 |
| TaqMan gene expression assay (cdkn1a-FAM) | Applied Biosystems | Mm00432448_m1 |
| TaqMan gene expression assay (cdkn1b-FAM) | Applied Biosystems | Mm00438168_m1 |
| TaqMan gene expression assay (cdkn1c-FAM) | Applied Biosystems | Mm00438170_m1 |
| TaqMan gene expression assay (GADPH-VIC) | Applied Biosystems | 4352339E |
| Software and Algorithms | ||
| Flowjo | FlowJo, LLC | www.flowjo.com |
| Cytobank | 65 | www.cytobank.org |
| Matlab or R – Normalizer | 70 |
https://github.com/nolanlab/bead-normalization/wiki/Normalizing-FCS-Files
https://github-com.laneproxy.stanford.edu/ParkerICI/premessa—R |
| Matlab or R – Single Cell Debarcoder | 66 |
https://github.com/nolanlab/single-cell-debarcoder
https://github-com.laneproxy.stanford.edu/ParkerICI/premessa—R |
| Vortex | 67 | https://github.com/nolanlab/vortex/ |
| STAR | 68 | https://github.com/alexdobin/STAR/releases |
| RSEM | 69 | https://github.com/bli25ucb/RSEM_tutorial |
| DESeq2 | 70 | http://www.bioconductor.org/packages/DESeq2/ |
| Living Image v.4.5 | Perkin Elmer | Perkinelmer.com |
| Aurora Scientific Dynamic Muscle Data Acquisition and Analysis Software | Aurora Scientific | https://aurorascientific.com/products/muscle-physiology/muscle-daq-software/615a-dynamic-muscle-control/ |
| Keyence Analysis Software (BZ-X700 Microscope) | Keyence | www.keyence.com |
| CRISP | 71 | github.com/will-yx/ |
| FiberNet | 71 | github.com/will-yx/ |
| Graphpad Prism 9 | GraphPad Software, Inc | www.graphpad.com |