KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-γH2AX (20E3) | Cell Signaling | Cat# 9718 (1:250 dilution for IF) |
| Rabbit anti-HMGB1 | Abcam | Cat# ab18256 (1:500 dilution for IF) |
| Rabbit anti-LaminB1 | Abcam | Cat# ab16048 (1:500 dilution for IF) |
| Rabbit anti-P21 | Abcam | Cat# ab109199 (1:200 dilution for IF) |
| Mouse anti-P21 | Santa Cruz | Cat# sc-53870 (1:500 for western blot) |
| Rabbit anti-GAPDH | Cell Signaling | Cat# 5174 (1:20,000 for western blot) |
| Rabbit anti-Laminin | Sigma | Cat# L9393 (1:100 dilution for IF) |
| Mouse anti-P16 | CINTec Histology, Roche | Cat# 9511 (IF, dilution as provided by manufacturer) |
| Wheat Germ Agglutinin, Alexa Fluo 488 Conjugate | Invitrogen | Cat# W11261 (1:750 dilution for IF) |
| Goat anti-rabbit Fluorescein-conjugated secondary antibody Alexa Fluor 488 | Invitrogen | Cat# A11008 (1:500 dilution for IF) |
| Goat anti mouse biotinylated secondary antibody | Vector Laboratories | Cat# AI-9200 (1:200 dilution for IHC) |
| Goat anti-rabbit biotinylated secondary anti-body | Vector Laboratories | Cat# PK-6101 (1:200) |
| m-IgGκ BP-HRP | Santa Cruz | Cat# sc-516102 (1:20,000 for western blot) |
| mouse anti-rabbit IgG-HRP | Santa Cruz | Cat# sc-2357 (1:20,000 for western blot) |
| Rabbit anti-rabbit Fluorescein-conjugated secondary antibody Alexa Fluor 594 | Invitrogen | Cat# A11012 (1:500 dilution for IF) |
| Rabbit anti-rabbit Fluorescein-conjugated secondary antibody Alexa Fluor 647 | Invitrogen | Cat# A21245 (1:500 dilution for IF) |
| Rabbit anti-mouse Fluorescein-conjugated secondary antibody Alexa Fluor 594 | Invitrogen | Cat# A44005 (1:500 dilution for IF) |
| Rabbit anti-guinea pig Fluorescein-conjugated secondary antibody Alexa Fluor 594 | Invitrogen | Cat# A11076 (1:500 dilution for IF) |
| CD31 MicroBeads, mouse | Miltenyi | Cat# 130-097-418 |
| CD45 MicroBeads, mouse | Miltenyi | Cat# 130-052-301 |
| Anti-Sca-1 (non-HSC) MicroBeads, mouse | Miltenyi | Cat# 130-106-641 |
| Anti-Integrin α-7 (Integrin Subunit Alpha 7) MicroBeads, mouse | Miltenyi | Cat# 130-104-261 |
| Primers for qPCR | ||
| Tbp | Integrated DNA Technologies | Cat# MM.PT.39a.22214839 |
| Gapdh | Integrated DNA Technologies | Cat# Mm.PT.39a.1 |
| p16Ink4a | Integrated DNA Technologies | Cat# MM.PT.58.42804808 |
| p21 | Integrated DNA Technologies | Cat# MM.PT.58.5884610 |
| p21 variant 2 | Integrated DNA Technologies | Cat# Mm.PT.58.31908645 |
| Ccl2 | Integrated DNA Technologies | Cat# MM.PT.58.42151692 |
| Tnfa | Integrated DNA Technologies | Cat# Mm.PT.58.12575861 |
| Tgfb | Integrated DNA Technologies | Cat# Mm.PT.58.11254750 |
| Il1a | Integrated DNA Technologies | Cat# Mm.PT.58.32778767 |
| Il6 | Integrated DNA Technologies | Cat# Mm.PT.58.10005566 |
| Pai1 | Integrated DNA Technologies | Cat# Mm.PT.58.6413525 |
| Mmp3 | Integrated DNA Technologies | Cat# Mm.PT.58.9719290 |
| Mmp9 | Integrated DNA Technologies | Cat# Mm.PT.58.10100097 |
| Cd31 | Integrated DNA Technologies | Cat# Mm.PT.58.12394061 |
| Cd68 | Integrated DNA Technologies | Cat# Mm.PT.58.32698807 |
| Pax7 | Integrated DNA Technologies | Cat# Mm.PT.58.12398641 |
| Runx1 | Integrated DNA Technologies | Cat# Mm.PT.58.5873245 |
| Ankrd1 | Integrated DNA Technologies | Cat# Mm.PT.58.11977470 |
| Gadd45a | Integrated DNA Technologies | Cat# Mm.PT.58.42316074 |
| Rrad | Integrated DNA Technologies | Cat# Mm.PT.58.10415826 |
| Pdgfra | Integrated DNA Technologies | Cat# Mm.PT.56a.5639577 |
| TBP (human) | Integrated DNA Technologies | Cat# Hs.PT.58.20792004 |
| P16Ink4a (human) | Integrated DNA Technologies | Sequence F: 5’ CCAACGCACCGAATAGTTACG 3’ R: 5’ GCGCTGCCCATCATCATG 3’ P: 5’ FAM - CCTGGATCGGCCTCCGAC - MGB 3’ |
| Chemicals, Peptides, and Recombinant Proteins, and Commercial Assays | ||
| Collagenase II | Worthington Biochemical Corporation | Cat# LS004176 |
| bFGF Recombinant Human Protein | Gibco | Cat# 13256029 |
| Chick Embryo Extract | Life Science Group | Cat# MD-004E-UK |
| TRIzol reagent | Invitrogen | Cat# 15596026 |
| miRNeasy Mini Kit | Qiagen | Cat# 217004 |
| Red Blood Cell Lysis Solution | Miltenyi | Cat# 130-094-183 |
| M-MLV Reverse Transcriptase | Invitrogen | Cat# 28025013 |
| PerfeCTa qPCR FastMix II, ROX, QuantaBio | Quantabio | Cat# 95119-05K |
| Skeletal Muscle Dissociation Kit | Miltenyi | Cat# 130-098-305 |
| RNAscope Multiplex Fluorescent v2 Assay | Advanced Cell Diagnostics | Cat# 323100-USM |
| RNAscope probe targeting p21 (Mm-Cdkn1a) | Advanced Cell Diagnostics | Cat# 408551 |
| Cy-3-labelled telomere-specific (CCCTAA) peptide nucleic acid probe | PANAGENE | Cat# F1002 |
| CENPB-FAM centromere specific probe | PANAGENE | Cat# F3001 |
| SMART-Seq v4 Ultra Low Input RNA Kit | Clontech | Cat# 634888 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat# FC-131-1096 |
| TruSeq Stranded mRNA Sample Prep Kit | Illumina | Cat# 20020594 |
| Chromium Single Cell 3’ Reagent Kits | 10X Genomics | Cat# PN-1000075 |
| M.O.M. (Mouse on Mouse) Immunodetection Kit, Basic | Vector Laboratories | Cat# BMK-2202 |
| Avidin/Biotin Blocking Kit | Vector Laboratories | Cat# SP-2001 |
| Vector NovaRED Peroxidase (HRP) Substrate Kit | Vector Laboratories | Cat# LS-J1084 |
| Fluorescein Avidin DCS | Vector Laboratories | Cat# SP-2011 |
| Sudan Black B | Frontier scientific | Cat# JK226545 |
| ProLong™ Gold Antifade Mountant with DAPI | Invitrogen | Cat# P36935 |
| SuperSignal West Pico PLUS Chemiluminescent Substrate | Thermo Scientific | Cat# 34577 |
| Protease inhibitor cocktail | Sigma | Cat# P8340 |
| PMSF | Thermo Scientific | Cat# 36978 |
| DC Protein Assay | Bio-Rad | Cat# 5000116 |
| PVDF membrane | Bio-Rad | Cat# 1620177 |
| Cell Lysis Buffer | Cell Signaling | Cat# 9803 |
| Deposited Data | ||
| RNA-seq data of isolated myofibers | GEO database | GEO: GSE172254 |
| RNA-seq data of skeletal muscle from young, old-Vehicle, and old-DQ mice | GEO database | GEO: GSE184348 |
| scRNA-seq data of skeletal muscle from young and old mice | GEO database | GEO: GSE172410 |
| Interactive website for scRNA-seq data | https://mayoxz.shinyapps.io/Muscle/ | |
| Experimental Models: Organisms/Strains | ||
| Mouse: WT C57BL6/J | The Jackson Laboratory & NIA | Cat# JAX:000664 |
| Software and Algorithms | ||
| Prism | Graphpad | RRID:SCR_002798; V8.4.1 |
| ImageJ | https://imagej.net/ | RRID:SCR_003070; V2.0.0-rc-64/1.51s |
| Fiji | http://fiji.sc | RRID:SCR_002285; V2.0.0-rc-69/1.52p |
| Metamorph | http://www.moleculardevices.com/Products/Software/Meta-Imaging-Series/MetaMorph.html | RRID:SCR_002368; VV7.10.2 |
| Cell Ranger | 10X Genomics | RRID:SCR_017344; V3.0 |
| R | https://www.r-project.org/ | RRID: SCR_001905; V3.6.0 |
| Seurat | https://satijalab.org/seurat/ | RRID: SCR_016341; V3.1.3 |
| Tophat2 | http://ccb.jhu.edu/software/tophat/index.shtml | RRID:SCR_013035; V2.1.1 |
| RSeQC | http://code.google.com/p/rseqc/ | RRID:SCR_005275; V2.3.6 |
| edgeR | http://bioconductor.org/packages/edgeR/ | RRID:SCR_012802; V3.10 |
| Clusterprofiler | http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html | RRID:SCR_016884; V3.18.1 |
| GSEA | Broad Institute | RRID: SCR_003199; V4.0.3 |
| Cellchat | http://www.cellchat.org/ | V1.0.0 |
| Others | ||
| CellAge_Senescence_UP gene set | https://genomics.senescence.info/cells/ | |
| PanglaoDB | https://panglaodb.se/ |