KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological Samples | ||
| C57BL/6J (8 weeks) | The Jackson Laboratory | https://www.jax.org/ |
| C57BL/6J (26 weeks) | The Jackson Laboratory | https://www.jax.org/ |
| C57BL/6J (60 weeks) | The Jackson Laboratory | https://www.jax.org/ |
| C57BL/6J (78 weeks) | The Jackson Laboratory | https://www.jax.org/ |
| C57BL/6J (104 weeks) | The Jackson Laboratory | https://www.jax.org/ |
| Critical Commercial Assays | ||
| NucleoSpin RNA kits | Macherey-Nagel | 740406.50 |
| Antisense Oligo | IDT | https://sg.idtdna.com/pages |
| TRI Reagent | Sigma-Aldrich | T9424 |
| Deposited Data | ||
| RNA-seq raw data are available at NGDC (https://bigd.big.ac.cn/) under the BioProject accession number PRJCA002140 | This paper | NGDC: PRJCA002140 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | https://www.jax.org/ |
| Software and Algorithms | ||
| Quality control of RNA-seq: fastqc v.0.11.2 | Andrews, 2010 | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| RNA-seq Mapping: STAR v.2.6.0c | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| Counting reads: featureCounts v.1.6.3 | Liao et al., 2014 | http://subread.sourceforge.net/ |
| R system: R v3.4.5 | N/A | https://cran.r-project.org/ |
| Programming environment of R: RStudio v1.2.5001 | N/A | https://rstudio.com/ |
| Differential gene expression analysis: limma v.3.34.9 | Law et al., 2016 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| Differential gene expression analysis: edgeR v.3.20.9 | Robinson et al., 2010. | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| Functional annotation: DAVID v.6.8 | Huang et al., 2009 | https://david.ncifcrf.gov/ |
| Gene expression interaction: Hmisc v.4.2 | Harrell, 2019 | https://cran.r-project.org/web/packages/Hmisc/index.html |
| Network cluster: igraph v.1.2.4.1 | Csardi and Nepusz, 2006 | https://igraph.org/redirect.html |
| Network Dynamic Visualizations: ndtv v.0.12.3 | Bender-deMoll, 2016 | https://github.com/statnet/ndtv |
| Data visualization: ggplot2 v.3.2.0 | Wickham, 2016 | https://ggplot2.tidyverse.org/ |
| Data visualization: gplots v.3.0.1.1 | Warnes et al., 2019 | https://cran.r-project.org/web/packages/gplots/index.html |
| Data visualization: ComplexHeatmap v.2.1.0 | Gu et al., 2016 | https://github.com/jokergoo/ComplexHeatmap |
| Data visualization: pheatmap v.1.0.12 | Kolde, 2019 | https://github.com/raivokolde/pheatmap |