KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-BMAL1 (ChIP-Seq) | J. Bass, Millipore | ABE2599 (Perelis et al., 2015) |
| Anti-BMAL1 (WB) | Santa Cruz | sc-48790 |
| Anti-HSF1 | Cell Signaling | 4356 |
| Anti-H3 | Cell Signaling | 9715 |
| Anti-H3K27Ac | Active Motif | 39133 |
| Anti-H3K9Ac | Active Motif | 39137 |
| Anti-β-ACTIN | Cell Signaling | 4970 |
| Anti-GAPDH | Cell Signaling | 5174 |
| Anti-p-PER2-S659 | Thermo Fisher | PA5-38901 |
| Anti-PER2 | C. Lee (Florida State University) | |
| Anti-PER1 | Abcam | ab136451 |
| Anti-CRY2 | Alpha Diagnostic | CRY21-A |
| Anti-CRY1 | Bethyl | A302-614A |
| Anti-FLAG-HRP | Sigma | F1804-50UG |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Tamoxifen | Sigma | T5648-1G |
| Corn Oil | Sigma | C8267-500ML |
| Trypsin | Fisher Scientific | 25300054 |
| Dexamethasone | Sigma | D4902-100MG |
| Nicotinamide mononucleotide (NMN) | Oriental Yeast Company | 44500900-1g |
| PBS | Mediatech | 21-040-CM |
| Nicotinamide riboside (NR) | Chromadex | N001 |
| Perchloric acid | Sigma | 244252-100ML |
| K2CO3 | Sigma | 367877-10G |
| Trizol Reagent | Molecular Research Center | TR118 |
| Disuccinimidyl glutarate | Proteochem | C1104-1 gram |
| DMSO | Sigma | D8418-100ML |
| Formaldehyde | Polysciences | 18814 |
| Sodium chloride (NaCl) | Fischer Scientific | BP35-10 |
| Ethylenediaminetetraacetic acid (EDTA) | Lonza | 51234 |
| Trizma® hydrochloride solution | Millipore-Sigma | T2319-1L |
| NP-40 | Sigma | NP40s |
| SDS | Sigma | L3771-ikg |
| Triton X-100 | Sigma | X100-100ML |
| MgCl2 | Sigma | M8266 |
| IGEPAL | Sigma | I8896-50ML |
| Tween-20 | Sigma | P1754-500ML |
| Digitonin | Sigma | D141-100MG |
| Nextera transposase enzyme | Illumina | 15027865 |
| Nextera TD buffer | Illumina | 15027865 |
| FK866 | Sigma | F8557-25MG |
| EX527 | Tocris | 2780 |
| HEPES | Gibco | 15630080 |
| NE-PER kit | ThermoFisher | 78835 |
| B27 Supplement | Invitrogen | 17504-001 |
| Trichostatin A | Sigma | T8552-1MG |
| Nicotinamide | Sigma | N3501-100MG |
| Ammonium bicarbonate | ThermoFisher | A643500 |
| Acetonitrile | ThermoFisher | A955500 |
| Dithiothreitol | Thermo Fisher | R0861 |
| Ambic/iodoacetamide | Sigma | I1149-5G |
| Formic acid | ThermoFisher | P128905 |
| Dulbecco’s modified Eagle’s medium (DMEM) | Gibco | MT10013CV |
| Sodium bicarbonate | Sigma | S5761-500G |
| Fetal bovine serum (FBS) | Atlanta Biological | S11550 |
| Penicillin-Streptomycin | Gibco | 15140122 |
| Luciferin sodium salt | Biosynth AG | L8220 |
| Cycloheximide | Sigma | 239764-1GM |
| Protease inhibitor cocktail, Complete mini | Roche Applied Science | 11836170001 |
| Phosphatase inhibitor cocktail, phoSTOP | Roche Applied Science | 04906845001 |
| Anti-FLAG conjugated paramagnetic beads | Sigma | M8823-1ML |
| L-Glutamine | Thermo Fisher Scientific | 25030081 |
| Sucrose | Sigma | S7903-1KG |
| KH2PO4 | Sigma | P3786-100g |
| Palmitoyl-carnitine | Sigma | P1645-5MG |
| Oligomycin | Sigma | O4876-5MG |
| FCCP | Sigma | C2920-10MG |
| Antimycin A | Sigma | A8674-25MG |
| Mannitol | Sigma | M9546-250G |
| EGTA | Bostonbioproducts | BM-151 |
| Fatty acid-free BSA | Sigma | A7511-5G |
| Critical Commercial Assays | ||
| Zymo Direct-Zol RNA miniprep kit | Zymo Research | R2051 |
| NEBNext RNA Ultra Directional Library Preparation Kit | New England Biolabs | E7420S |
| NEBNext Library Quant Kit | New England Biolabs | E7630S |
| NEBNext Ultra II Library Prep Kit | New England Biolabs | E7645S |
| Q5 site directed mutagenesis kit | New England Biolabs | E0552S |
| MinElute columns | Qiagen | 28006 |
| Software and Algorithms | ||
| Bowtie (v2.2.4) | http://bowtie-bio.sourceforge.net/index.shtml | (Langmead et al., 2009) |
| subread:featureCounts (v1.5.1). | (Liao et al., 2014) | |
| STAR (v2.5.2) | (Dobin et al., 2013) | |
| DESeq2 (v1.24.0) | (Love et al., 2014) | |
| eJTK_Cycle (v3.1.R). | (Hutchison et al., 2015) | |
| ClockLab Data Collection and Analysis System (v6.0) | http://actimetrics.com | |
| R Package ATACSeqQC | (Ou et al., 2018) | |
| HOMER (v4.10) | http://homer.ucsd.edu/homer/index.html | (Heinz et al., 2010) |
| Xcalibur (v4.0) | ||
| Mascot search engine (v2.5.1). | Matrix Science, London, UK | |
| MS/MS spectra scaffold (v4.8.3) | Proteome Software, Portland, OR | |
| Deposited Data | ||
| RNA-seq, ChIP-seq, ATAC-seq | NCBI GEO | GSE133989 |
| Experimental Models (Cells) | ||
| Per2::Luciferase MEFs | J. Takahashi (UT Southwestern) | |
| Sirt1−/− MEFs | J. Bass Lab | Harvested from Sirt1fx/fx mice treated with 3 rounds Adeno-Cre (Vector Biolabs) |
| HEK293 cells | Clontech | |
| Experimental Models (Mice) | ||
| C57BL/6CR (4 mo, 16 mo) | Charles River, NIA Colony | |
| Bmal1−/− | J. Takahashi (UT Southwestern) | |
| Per2::Luciferase | J. Takahashi (UT Southwestern) | |
| Namptfx/fx | S. Imai (Washington University) | |
| Sirt1fx/fx | S. Imai (Washington University) | |
| Alb-Cre | Jackson Laboratories | |
| CAGCre-ER | Jackson Laboratories | |
| Recombinant DNA | ||
| shRNA targeting p19ARF | Addgene | 14090 |
| pCMV-SPORT2-PER2 | Addgene | 16204 |