Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited data | ||
| RNA-seq of mice and Blind mole rats | Gene Expression Omnibus | GSE181413 |
| RNA-seq with different interventions in mouse liver | Gene Expression Omnibus | GSE131901 |
| Circadian RNA-seq data in mouse liver | Gene Expression Omnibus | GSE39860 |
| Circadian ChIP-seq data in mouse liver | Gene Expression Omnibus | GSE39977 |
| CLOCK ChIP-seq data in mouse liver | Gene Expression Omnibus | GSE53828 |
| OCT4 binding and Histone modification profiling during OSKM-mediated reprogramming | Gene Expression Omnibus | GSE67520 |
| ArrayExpress of OSKM-mediated reprogramming cells and the corresponding iPS cell line | Gene Expression Omnibus | GSE67462 |
| RNA-seq of mouse pre-implantation embryos | Gene Expression Omnibus | GSE66390 |
| RNA-seq of gastrulation in mouse | Gene Expression Omnibus | GSE76505 |
| RNA-seq of mouse tissues during aging | Gene Expression Omnibus | GSE132040 |
| RNA-seq of fetal mouse tissues | encodeproject.org | Heart, Limb, Liver, Lung and Kidney tissues: Barbara Wold, Caltech; Whole Brain: Bing Ren, UCSD |
| RNA-seq of human tissues during aging | The Genotype-Tissue Expression (GTEx) project | GTEx_Analysis_2017–06-05_v8_ |
| RNA-seq used for MLS gene identification | This study | GSE190756 |
| RNA-seq of Interfollicular Epidermal Stem Cells | Gene Expression Omnibus | GSE92423 |
| RNA-seq of Hair Follicle Stem Cells | Gene Expression Omnibus | GSE92423 |
| RNA-seq of mesenchymal stem cells | Gene Expression Omnibus | GSE156174 |
| RNA-seq of skeletal stem cells | Gene Expression Omnibus | GSE156174 |
| RNA-seq of neural stem cells | Gene Expression Omnibus | GSE156407 |
| RNA-seq of hematopoietic stem cells | Gene Expression Omnibus | GSE164284 |
| RNA-seq of adipose derived stem cells | Gene Expression Omnibus | GSE171946 |
| RNA-seq of skeletal muscle stem cells | Gene Expression Omnibus | GSE178070 |
| RNA-seq of melanocyte stem cells | Gene Expression Omnibus | GSE96966 |
| RNA-seq of Spermatogonial stem cells and Female germline stem cells | Gene Expression Omnibus | GSE134640 |
| Experimental models: Organisms/strains | ||
| Norway rats | Charles River Laboratories | N/A |
| Golden hamsters | Charles River Laboratories | N/A |
| Capybaras | Bio Fau Assesoria e Comercio | N/A |
| Pacas | São Paulo State University | N/A |
| Guinea pigs | Elm Hill Labs | |
| Beavers | Wild caught in New York State | N/A |
| Chinchillas | Moulton Chinchilla Ranch | N/A |
| Deer mice | Wild caught in New York State | N/A |
| Muskrats | Wild caught in New York State | N/A |
| Woodchucks | Wild caught in New York State | N/A |
| Chipmunks | Wild caught in New York State | N/A |
| Eastern mole | Wild caught in New York State | N/A |
| Wild mice | Wild caught in New York State | N/A |
| Star-nosed mole | Wild caught in New York State | N/A |
| Red squirrels | Wild caught in New York State | N/A |
| Gray squirrels | Wild caught in New York State | N/A |
| Nutria | USDA Nutria Eradication Program | N/A |
| Blind mole rats | Wild caught in Upper Galilee Mountains in Israel | N/A |
| Bushy tail rats | Cascade Biological Supply | N/A |
| Naked mole rats | University of Rochester | N/A |
| African spiny mice | Texas Exotic animals | N/A |
| Octodon degus | Gift from Dr. Nattan Insel, University of Montana | N/A |
| Chinese hamster | Gift from Dr. Sarelius Lab, University of Rochester | N/A |
| Damara mole-rat | University of Rochester | N/A |
| Ellobius lutescens | Dr. Goskun lab, Turkey | N/A |
| Short-tailed Shrew | Wild caught in Auburn, AL | N/A |
| Software and algorithms | ||
| Trim_Galore | Babraham Bioinformatics | version 0.6.6 |
| HISAT2 | Kim Lab at UT Southwestern Medical Center, (Kim et al., 2019) | v2.2.1 |
| StringTie | The Center for Computational Biology, Johns Hopkins University, (Kovaka et al., 2019) | v2.1 |
| CD-HIT | Godzik’s Lab at the Burnham Institute, (Fu et al., 2012) | v4.8.1 |
| Gencode | The GENCODE Project, (Frankish et al., 2019) | mV25 |
| Nucleotide BLAST | National Center for Biotechnology Information, (Camacho et al., 2009) | v2.10.1 |
| Salmon | Dr.Rob Patro, Stony Brook University, (Patro et al., 2017) | v1.4.0 |
| pheatmap | Raivo Kolde, University of Tartu | v1.0.12 |
| R | The R Project for Statistical Computing | V4.03 |
| APE | http://ape-package.ird.fr/ (Paradis and Schliep, 2019) | V5.5 |
| phyloT | https://phylot.biobyte.de/ | V2 |
| VertLife | https://vertlife.org/ (Upham et al., 2019) | N/A |
| GSEA | UC San Diego and Broad Institute | V4.1 |
| EnrichmentMap | https://www.baderlab.org/Software/EnrichmentMap (Reimand et al., 2019) | V3.3 |
| DESeq2 | (Anders and Huber, 2010) | V1.34.0 |
| edgeR | (Robinson et al., 2010) | V3.14 |
| Integrative Genomics Viewer | Broad Institute | V2.9.2 |
| UpSet2 | https://vdl.sci.utah.edu/upset2/ (Lex et al., 2014) | Last updated on December 22, 2021 |
| ClusterProfiler | (Wu et al., 2021) | V3.14 |
| LISA | (Qin et al., 2020) | LISA v2.2.5 |
| Cytoscape | https://cytoscape.org/ | V3.8.2 |