| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-trimethyl-Histone H3(Lys4) rabbit polyclonal [Dilution - 1: 100] | EMD Millipore | 07–473 (Lot: 3394198); RRID: AB_1977252 |
| Anti-trimethyl-Histone H3 (Lys27) C36B11 rabbit monoclonal [Dilution - 1: 100] | Cell Signaling Technology | 9733S; RRID: AB_2616029 |
| Anti-NELF-E Rabbit Polyclonal [Dilution - 1: 100] | ProteinTech | 10705-1-AP; RRID:AB_513966 |
| Guinea Pig Anti-rabbit IgG (Heavy & Light Chain Antibody) [Dilution - 1: 100] | Antibodies-online | ABIN101961; RRID: AB_10775589 |
| Rabbit Anti-Mouse IgG [Dilution - 1: 100] | Abcam | Ab46540; RRID: AB_2614925 |
| Anti-Alpha 7 Integrin 647 (clone R2F2) [Dilution - 1: 300] | ABLab | 67-0010-05; RRID: AB_2890939 |
| Biotin Rat Anti-Mouse CD45 Clone 30-F11 (RUO) [Dilution - 1: 100] | BD Pharmingen | 553077 |
| Biotin Rat Anti-Mouse CD31 Clone MEC 13.3 (RUO) [Dilution - 1: 100] | BD Pharmingen | 553371; RRID: AB_394817 |
| Ly-6A/E (Sca-1) Monoclonal Antibody (D7), Biotin eBioscienceTM [Dilution - 1: 100] | Thermo Fisher Scientific | 13–5981-81; RRID: AB_466833 |
| PE Streptavidin [Dilution - 1: 100] | BD Pharmingen | 554061 |
| PE/Cyanine7 anti-mouse CD106 Antibody [Dilution - 1: 100] | BioLegend | 105720; RRID: AB_2214046 |
| Bacterial and virus strains | ||
| T7 Express lysY/Iq Competent E. coli | NEB | C3013I |
| Chemicals, peptides, and recombinant proteins | ||
| Isoflurane USP | Fresenius Kabi Canada | Product code: CP0406V2 |
| Bupenorphine (Controlled Substance – needs permit) | Comparative Medicine and Animal Resource Center - McGill University | N/A |
| Collagenase from Clostridium histolyticum, Type I | Sigma-Aldrich | C0130-1G |
| Dispase II (Neutral Protease, grade II) | Roche | 04942078001 |
| SYTOX Green | Life Technologies | S7020 |
| 7-AAD (7-Aminoactinomycin D) | Stem Cell Technologies | 75001 |
| Hams F10 | Wisent Biocenter | 318-050-CL |
| Bovine Growth Serum/Bovine Calf Serum (BGS) | HyClone Fisher Scientific | SH3054103 |
| D-PBS | Life technologies | 21600010 |
| Cardiotoxin | Latoxan | L8102-1MG |
| 0.9% Saline solution (0.9% Bacteriostatic Sodium Chloride Injection USP) | Pfizer | NDC 0409-1966-12 |
| HEPES potassium salt | Sigma-Aldrich | H0527-250G |
| Sodium chloride | Sigma-Aldrich | S9625-1KG |
| Potassium chloride | Sigma-Aldrich | P9541-1KG |
| Calcium chloride | Sigma-Aldrich | C3306-500G |
| Magnesium chloride | Sigma-Aldrich | M2670-500G |
| Manganese Chloride | BioShop | MAN 222 |
| Bovine Serum Albumin | Sigma-Aldrich | A9647 |
| Digitonin | EMD- Millipore | 300410-1GM |
| Red Blood Cell Lysis Buffer Hybri-Max | Sigma-Aldrich | R7757-100ML |
| Roche Complete Protease Inhibitor EDTA-Free tablets | Sigma-Aldrich | 5056489001 |
| Spermidine | Sigma-Aldrich | S2626 |
| BioMag®Plus Concanavalin A (3 or 10mL) | Bangs Laboratories | BP531 |
| Ethylenediaminetetraacetic Acid Disodium Salt Dihydrate | Fisher Chemicals | S311-500 |
| Dimethyl Sulfoxide | Sigma-Aldrich | D8418-100ML |
| Triton-X-100 | Sigma-Aldrich | T8787-250ML |
| Glycerol | Fisher Chemicals | G33-1 |
| Sodium dodecyl sulfate | Bio-Rad | 1610302 |
| Proteinase K | BioShop | PRK403.100 |
| Phenol-chloroform-isoamyl alcohol | Fisher Scientific | BP1752I-400 |
| Chloroform | Sigma-Aldrich | 319988 |
| Ethanol | Greenfield Specialty Alcohol INC | P016EAAN |
| Glycogen | Santa Cruz Biotechnology | SC-203976 |
| RNase A | Sigma-Aldrich | R4642 |
| Trizma Base | Sigma-Aldrich | T6066-1KG |
| Kapa Pure Beads | Roche | 7983271001 |
| Critical commercial assays | ||
| PowerUp™ SYBR™ Green Master Mix | Thermo Fisher Scientific | A25742 |
| NEBNext High-Fidelity 2× PCR Master Mix | NEB | M0541L |
| QIAquick Gel Extraction Kit | QIAGEN | 28704 |
| QIAquick PCR Purification Kit | QIAGEN | 28104 |
| MaXtract High Density | QIAGEN | 129046 |
| Qubit™ 1× dsDNA HS Assay Kit | Thermo Fisher Scientific | Q33230 |
| NEBNext® Library Quant Kit for Illumina® | NEB | E7630L |
| Bioanalyzer High Sensitivity DNA Analysis | Agilent | Part number: 5067-4627 |
| Experimental models: organisms/strains | ||
| Mouse strain: Pax7gCre/gCre TdTFl/Fl: | Bred for this paper | N/A |
| Mouse strain: B6.Cg-Pax7tm1(cre/ERT2)Gaka/J | The Jackson Laboratory | JAX 017763 |
| Mouse strain: B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J | The Jackson Laboratory | JAX 007909 |
| Oligonucleotides | ||
| Mosaic end_Adapter A (ME-A): TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG |
IDT | Custom |
| Mosaic end_Adapter B (ME-B): GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG |
IDT | Custom |
| Mosaic end_reverse (ME-Reverse): [PHO]CTGTCTCTT ATACACATCT |
IDT | Custom |
| Tn5 ME-A Amp Forward: TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GATACGGGAGGGCTTACCAT |
IDT | Custom |
| Tn5 ME-B Amp Reverse: GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA G GGATGGAGGCGGATAAAGTT |
IDT | Custom |
| Recombinant DNA | ||
| Spike-inAmpR | This Paper | N/A |
| Software and algorithms | ||
| FastQC v0.11.9 | (Babraham Bioinformatics, 2019) | https://www.bioinformatics.babraham.ac.uk/projects/download.html |
| MultiQC | (Ewels et al., 2016) | https://multiqc.info/ |
| Cutadapt | (Martin, 2011) | https://cutadapt.readthedocs.io/en/stable/ |
| Bowtie2 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Samtools | (Li et al., 2009) | http://samtools.sourceforge.net/ |
| Picard Tools | (Broad Institute, 2012) | https://broadinstitute.github.io/picard/ |
| DeepTools | (Ramirez et al., 2016) | https://deeptools.readthedocs.io/en/develop/ |
| SEACR | (Meers et al., 2019) | https://seacr.fredhutch.org/ |
| BEDtools | (Quinlan and Hall, 2010) | https://bedtools.readthedocs.io/en/latest/ |
| BedToBigBed | (Kent et al., 2002) | https://www.encodeproject.org/software/bedToBigBed/ |
| ChIPSeeker | (Yu et al., 2015) | https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
| Other | ||
| 3/10 cc Insulin Syring U-100 29G1/2" | BD/Fisher Scientific | 309301 |
| 3 mL Syringes | BD/Fisher Scientific | B309657 |
| Nair 3-in-1 hair removal lotion | Walmart | Item number: 4636345 |
| Dissection tools | Fisher Scientific | N/A |
| Thermo Steri-cycle CO2 Incubator | Thermo Electron Corporation | N/A |
| Tissue Culture Dish 60 | SARSTEDT AG & Co.KG | 83.3901 |
| 15 mL Conical Tubes | FroggaBio | TB15-500 |
| 50 mL Conical Tubes | FroggaBio | TB50-25 |
| Large volume centrifuge tube, 500 mL, Polypropylene | Corning | CLS431123-36EA |
| Nikon Eclipse TS100 Microscope | Nikon | N/A |
| NanoDropTM One Microvolume UV-Vis Spectrophotometer | Thermo Fisher Scientific | ND-ONE-W |
| Fisherbrand™ Hand Tally Counter | Fisher scientific | 079056 |
| Hausser Scientific Bright-Line™ Phase Hemacytometer | Fisher scientific | 026716 |
| PYREX® Round Media Storage Bottles, with Screw Cap | Corning | 1395-100; 1395-250; 1395-500 |
| BD 50 mL Syringe | BD Biosciences | 309653 |
| Filtropur S 0.2 μM Syringe Filters | SARSTEDT AG & Co.KG | 83.1826.001 |
| 5-mL Polypropylene Round Bottom Tube | Falcon | 352063 |
| Cell Strainer 40 μm | Fisher Scientific | 22363547 |
| CellTrics 50 μm | Sysmex Canada Inc | 04-004-2327 |
| 1.5 mL Microcentrifuge tubes | Axygen | MCT-175-CT |
| 50 mL, Polypropylene Bottle with Screw-On Cap, 29 X 104mm | Beckman Coulter | 357003 |
| Amicon Ultra-4 Centrifugal Filter Unit | Millipore | UFC803024 |
| Thermo ScientificTM Slide-A-LyzerTM Dialysis Cassettes, 10 K MWCO, 3 mL | Fisher Scientific | 66380 |
| Nutator Mixer | VWR | 82007-202 |
| Benchtop Orbital Shaker (w Temperature Chamber) | ThermoFisher | SHKE4000 |
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