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 |