| Reagent or resource | Source | Identifier |
|---|---|---|
| Chemicals, peptides, and recombinant proteins | ||
| Dispase II (activity ≥0.5 units/mg solid) | Sigma | D4693‐1G |
| Collagenase Type II | Life Technologies | 17101015 |
| DMEM, high glucose, pyruvate | Life Technologies | 11995065 |
| Ham's F‐10 Nutrient Mix | Life Technologies | 11550043 |
| HBSS, no calcium, no magnesium, no phenol red | Life Technologies | 14175145 |
| Saline Phosphate Buffered Gibco PBS (Phosphate Buffered Saline) Solution pH 7.4 No phenol red no sodium pyruvate | Thermo Fisher |
10010023 |
| Fetal bovine serum | Life Technologies | 10437028 |
| Digitonin | Fisher Scientific | BN2006 |
| Trizma hydrochloride Solution, pH 7.4 | Sigma Aldrich | T2194 |
| Sodium chloride Solution, 5 M | Sigma Aldrich | 59222C |
| Magnesium chloride solution, 1 M | Sigma Aldrich | M1028 |
| Nonidet P40 substitute | Sigma Aldrich | 492018‐50ML |
| Sigma protector RNase inhibitor | Sigma Aldrich | 3335402001 |
| DL‐DTT | Sigma Aldrich | 646563 |
| 7‐AAD | Biolegend | 420403 |
| MACS BSA stock solution | Miltenyi | 130‐091‐376 |
| New England Biolabs, Inc. supplier diversity partner BSA‐molecular biology grade ‐ 12 mg | Fisher Scientific |
NC0506695 |
| Tween‐20 | BioRad | 1662404 |
| 0.5 M EDTA | Qiagen | 79306 |
| Formaldehyde, 37% by weight (with preservative/certified ACS) | Fisher Chemical | F79‐500 |
| KAPA HiFi HotStart Library Amplification Kit with Primer Mix | Fisher Scientific |
50–196‐5224 |
| Agencourt AMPure XP | Beckman Coulter | A63881 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher | Q32851 |
| Antibodies | ||
| APC anti‐Mouse Ly‐6A/E (Sca‐1), clone: D7, isotype: Rat IgG2a, κ | BioLegend | 108112 |
| APC anti‐Mouse CD45, clone: 30‐F11, isotype: Rat IgG2b, κ | BioLegend | 103112 |
| APC anti‐Mouse/Human CD11b, clone: M1/70. Isotype: Rat IgG2b, κ | BioLegend | 101212 |
| APC anti‐Mouse TER‐119, clone: TER‐119, isotype: Rat IgG2b, κ | BioLegend | 116212 |
| PE anti‐Mouse/Rat CD29, clone: HMβ1‐1, isotype: Armenian Hamster IgG | BioLegend | 102208 |
| Biotin Rat Anti‐Mouse CD184, clone: 2B11/CXCR4 (RUO), isotype: Rat IgG2b, κ, lot # 6336587 | BD Bioscience | 551968 |
| Streptavidin PE‐Cyanine7, lot # 4290713 | eBioscience | 25–4317‐82 |
| 4′,6‐Diamidino‐2‐Phenylindole, Dihydrochloride (DAPI), FluoroPure™ grade | Invitrogen | D21490 |
|
PC anti‐mouse Ly‐6A/E (Sca‐1), clone: D7, isotype: Rat IgG2a, κ |
Biolegend | BioLegend 108112; RRID:AB_313349 |
| Critical commercial assays | ||
| Arima Hi‐C + Kit | Arima Genomics | 202012‐1415 |
| Accel‐NGS® 2 S Plus DNA library kit | Swift Biosciences | 21024 |
| 2 S Set A single indexed adapters | Swift Biosciences | 26148 |
| Chromium next GEM Single Cell ATAC Reagent Kit (v1.1) | 10x Genomics | PN‐1000175 |
| Experimental models: Organisms/Strains | ||
| Pax7CreER/+;Rosa26TdTomato/+ mice (24–29 months) | University of Michigan | Jackson stock 017763 crossed with stock 007676 |
| Pax7CreER/+;Rosa26TdTomato/+ mice (3–4 months) | University of Michigan | Jackson stock 017763 crossed with stock 007676 |
| Deposited data | ||
| Aging muscle stem Cell ATAC‐seq and RNA‐seq datasets |
Shcherbina et al. (2020), Cell Reports |
GSE121589 |
| Aging muscle stem cell single cell RNA‐seq datasets |
Larouche et al. (2021), eLife |
GSE165978 |
| Tabula Muris Senis Single cell droplet RNA‐seq datasets |
Almanzar et al. (2020), Nature |
GSE149590 |
| Aging muscle stem cell Hi‐C datasets | This Manuscript | GSE214047 |
| Software | ||
| Gene annotation | https://www.gencodegenes.org/mouse/release_M25.html | Gencode vM25 |
| Juicer | Durand, Shamim, et al. (2016) | Juicer Tools v1.22.01 |
| Juicebox | Durand, Robinson, et al. (2016) | Juicebox v1.11.08 |
| FAN‐C | Kruse et al. (2020) | FAN‐C v0.9.21 |
| HiCExplorer | Wolff et al. (2020) | HiCExplorer v3.7.2 |
| pyGenomeTracks | Ramírez et al. (2018); Lopez‐Delisle et al. (2021) | pyGenomeTracks v3.6 |
| MDkNN | Lin et al. (2022) | MDkNN v0.0.1 |
| Plotgardener | Kramer et al. (2022) | Plotgardener v1.2.10 |
| TOBIAS | Bentsen et al. (2020) | TOBIAS v0.13.3 |
| Cell Ranger ATAC | 10x Genomics | Cell Ranger ATAC v2.1.0 |
| Seurat | Stuart et al. (2019); Bioconductor | Seurat v4.1.1 |
| DoubletFinder | McGinnis et al. (2019) | DoubletFinder v2.0.3 |
| MACS2 | Zhang et al. (2008) | MACS2 v2.1.1 |
| GenomicInteractions | Harmston et al. (2015); Bioconductor | GenomicInteractions v1.28.0 |
| GenomicRanges | Lawrence et al. (2013); Bioconductor | GenomicRanges v1.46.1 |
| JASPAR TF Motifs | Castro‐Mondragon et al. (2022) | JASPAR CORE 2022 |
| ArchR | Granja et al. (2021) | ArchR v1.0.2 |
| Cicero | Pliner et al. (2018) | Cicero v1.3.6 |
| WebGestalt | Liao et al. (2019) | WebGestalt 2019 |
| ChIPseeker | Yu et al. (2015) | ChIPseeker v1.30.3 |
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