KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Chemicals, Peptides, and Recombinant Proteins | ||
|
| ||
| pEGFP-N2 | Addgene | Cat# 6081-1 |
| Dulbecco’s Modified Eagle Medium | Sigma-Aldrich | Cat# SLM-241-B |
| FBS | Thermo Fisher Scientific | Cat# 16000 |
| penicillin-streptomycin | Sigma-Aldrich | Cat# 516106 |
| rotenone | Sigma-Aldrich | Cat# 83-79-4 |
| Brefeldin A | Sigma-Aldrich | Cat# 20350-15-6 |
|
| ||
| Software and Algorithms | ||
|
| ||
| FlowJo | N/A | https://www.flowjo.com/solutions/flowjo/downloads |
| AllPath-LG | N/A | http://software.broadinstitute.org/allpaths-lg/blog/ |
| PBJelly | English et al., 2012 | https://sourceforge.net/p/pb-jelly/wiki/Home/ |
| Pilon | Walker et al., 2014 | https://github.com/broadinstitute/pilon |
| BWA-mem | Li and Durbin, 2009 | http://bio-bwa.sourceforge.net/ |
| SAMtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| 3D-dna | Dudchenko et al., 2017 | https://github.com/theaidenlab/3d-dna |
| BUSCO | Simão et al., 2015 | https://busco.ezlab.org/ |
| Maker2 | Holt and Yandell, 2011 | https://www.yandell-lab.org/software/maker.html |
| SNAP | Korf, 2004 | https://github.com/KorfLab/SNAP |
| AUGUSTUS | Stanke and Waack, 2003 | http://augustus.gobics.de/ |
| GeMoMa | Keilwagen et al., 2016 | http://www.jstacs.de/index.php/GeMoMa |
| SyMAP | Soderlund et al., 2011 | http://www.agcol.arizona.edu/software/symap/ |
| MCScanX | Wang et al., 2012 | http://chibba.pgml.uga.edu/mcscan2/ |
| proteinortho_v5.11 | Lechner et al., 2011 | https://www.bioinf.uni-leipzig.de/Software/proteinortho/older.html |
| Muscle | Edgar, 2004 | https://www.drive5.com/muscle/ |
| HYPHY | Pond et al., 2005 | http://www.hyphy.org/ |
|
| ||
| Deposited Data | ||
|
| ||
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182754 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182755 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182756 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182757 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182758 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182759 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182760 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182761 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182762 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182763 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182764 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182765 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182766 |
| PacBio reads of Naked mole rat | This paper | NCBI: SRR8182767 |
| Hic sequences of naked mole rat | This paper | NCBI: SRR8204318 |
| Assembled genome of American beaver | This paper | NCBI: RPDE00000000 |
| Assembled genome of naked mole rat | This paper | NCBI: RPGA00000000 |
|
| ||
| Experimental Models: Cell Lines | ||
|
| ||
| Mouse lung fibroblast cells | This paper | N/A |