Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background(M. musculus) | C57BL/6NIA | NIA Aged Rodent Colony | PMID:27549339 | |
| Strain, strain background(M. musculus) | C57BL/6J | Jackson Laboratory | RRID:IMSR_JAX:000664 | |
| Chemical compound, drug | Rapamycin | Rapamycin Holdings | Amount based upon active rapamycin content to provide 42 parts per million concentration in chow. | |
| Chemical compound, drug | Eudragit | Rapamycin Holdings | ||
| Chemical compound, drug | RIPA Lysis and Extraction Buffer | ThermoFisher Scientific |
Cat#: 89901 | |
| Chemical compound, drug | HALT Protease Inhibitor Cocktail |
ThermoFisher Scientific |
Cat#: 78438 | |
| Chemical compound, drug | HALT Phosphatase Inhibitor Cocktail | ThermoFisher Scientific |
Cat#: 78420 | |
| Chemical compound, drug | Restore Plus Stripping Buffer | Thermfisher Scientific | Cat#: 46430 | |
| Antibody | anti -NFkBp65(Rabbit Monoclonal) | Cell Signaling | Cat#: 8242 | WB (1:1000) |
| Antibody | anti-phospho-IκBα (Mouse monoclonal) | Santa Cruz Biotechnology |
Cat#: sc8404 | WB (1:1000) |
| Antibody | Anti- IκBα (Rabbit Monoclonal) |
Abcam | Cat#: 32518 | WB (1:1000) |
| Antibody | anti-GAPDH (Rabbit monoclonal) |
Cell Signaling | Cat#: 5174 | WB (1:1000) |
| Antibody | anti-RANKL (Mouse monoclonal) |
Santa Cruz Biotechnology | Cat#: sc377079 | WB (1:1000) |
| Antibody | anti-OPG (Goat polyclonal) |
R and D Systems | AF459 | WB (1:1000) |
| Antibody | anti-IgGκ (Mouse monoclonal) |
Santa Cruz Biotechnology | Cat#: sc516102 | WB (1:10000) |
| Antibody | anti-rabbit IgG (Donkey polyclonal) | Thermo Fisher Scientific | Cat#: 31458 | WB (1:10000) |
| Antibody | anti-goat IgG (Donkey polyclonal) |
Abcam | Cat#: ab97110 | WB (1:10000) |
| Commercial assay, kit | Proteome Profiler Mouse XL Cytokine Array | R and D Systems | Cat#: ARY028 | |
| Commercial assay, kit | Acid Phosphatase, Leukocyte (TRAP) Kit | Millipore Sigma | Cat#: 387A-1KT | |
| Commercial assay, kit | QIAamp DNA Microbiome Kit | Qiagen | Cat#: 51704 | |
| Commercial assay, kit | DNA Clean and Concentrator Kit | Zymo Research | Cat#: D4014 | |
| Commercial assay, kit | KAPA HiFi HotStart ReadyMix | KAPA Biosystems | Cat#: KK2601 | |
| Commercial assay, kit | Nextera XT Index Kit V2 | Illumina | Set A: FC-131–2001 Set D: FC-131–2004 |
|
| Commercial assay, kit | AMPure XP Beads | Agencourt | A63881 | |
| Commercial assay, kit | SequalPrep Normalization Kit | Invitrogen | A1051001 | |
| Commercial assay, kit | TapeStation 4200 High Sensitivity D1000 assay | Agilent Technologies | G2991AA | |
| Commercial assay, kit | Tapestation Reagents |
Agilent Technologies | 5067–5585 | |
| Commercial assay, kit | High Sensitivity D1000 ScreenTape | Agilent Technologies | 5067–5584 | |
| Commercial assay, kit | Qubit High Sensitivity dsDNA assay | ThermoFisher Scientific | Q32854 | |
| Commercial assay, kit | MiSeq Reagent Kit v3 (600 cycle) | Illumina | Cat#: MS-102–3003 | |
| Commercial assay, kit | PhiX Control Kit v3 | Illumina | Cat#: FC-110–3001 | |
| Software, Algorithm | Qiime2 | https://qiime2.org/ | V.2019.1 | |
| Software, Algorithm | DADA2 Package | PMID:27214047 | ||
| Software, Algorithm | Human Oral Microbiome Database (HOMD) |
Homd.org
PMID:30534599 |
v. 15.1 | |
| Software, Algorithm | R-studio | https://rstudio.com/ | RRID:SCR_000432 | Version 3.5.3 |
| Software, Algorithm | Phyloseq | PMID:23630581 | RRID:SCR_013080 | |
| Software, Algorithm | Clustvis | PMID:25969447 | RRID:SCR_017133 | |
| Software, Algorithm | Ggplot2 | https://www.springer.com/gp/book/9780387981413 | RRID:SCR_014601 | https://www.springer.com/gp/book/9780387981413 |
| Software, Algorithm | Ampvis2 | http://dx.doi.org/10.1101/299537v1 | ||
| Software, Algorithm | vegan | https://cran.r-project.org, https://github.com/vegandevs/vegan | RRID:SCR_011950 | |
| Software, Algorithm | Ade4 | https://www.jstatsoft.org/article/view/v086i01 | ||
| Software, Algorithm | Bioinformatic scripts and microbiome data used in analysis | This paper | https://github.com/kkerns85/Rapamycin_rejuvenates_oral_health_in_aging_mice.git. | |
| Software, Algorithm | R Markdown | This paper | https://rpubs.com/kkerns85/Rapamycin_Rmrkdown | |
| Software, Algorithm | Graphpad Prism | Graphpad (graphpad.com) | RRID:SCR_002798 | Version 8.4 |