| Antibodies |
| Mouse monoclonal anti-Poly-E-T (1:1000) |
AdipoGen |
Cat# AG-20B-0020-C100 |
| Mouse monoclonal anti-TUBB3 (1:1000) |
R&D Systems |
Cat# MAB1195 |
| Mouse monoclonal anti-OCT3/4 (1:500) |
Santa Cruz |
Cat# sc-5279 |
| Rabbit polyclonal anti-NANOG (1:500) |
Cosmo Bio |
Cat# RCAB0004P-F |
| Mouse monoclonal anti-ALBUMIN (1:500) |
Cedarlane |
Cat# CL2513A |
| Rabbit monoclonal anti-HNF4α (1:500) |
Cell Signaling |
Cat# 3113S |
| Rabbit polyclonal anti-DESMIN (1:500) |
Thermo Fisher |
Cat# RB9014P1 |
| Mouse anti-TNNT (1:500) |
Thermo Fisher |
Cat# MS295P0 |
| Rabbit polyclonal anti- Δ2-T (1:1000) |
Millipore |
Cat# AB3203 |
| Rabbit polyclonal anti-Poly-E-T (1:2000) |
AdipoGen |
Cat# AG-25B-0030-C050 |
| Rabbit polyclonal anti-TUBB3 (1:2000) |
BioLegend |
Cat# 802001 |
| Mouse monoclonal anti-TUBA (1:200) |
Sigma |
Cat# F2168 |
| Rabbit monoclonal anti-LAMP1 (1:1000) |
Cell Signaling |
Cat# 9091 |
| Rabbit polyclonal anti-VCP (p97) (1:1000) |
Cell Signaling |
Cat# 2648 |
| Mouse monoclonal anti-VCP (p97) (1:5000) |
Fitzgerald |
Cat# 10R-P104a |
| Mouse monoclonal anti-PSMB2 (1:1000) |
Santa Cruz |
Cat# SC-515066 |
| Mouse monoclonal anti-PSMB5 (1:1000) |
Santa Cruz |
Cat# SC-393931 |
| Mouse monoclonal anti-HSP60 (1:1000) |
Santa Cruz |
Cat# 4868 |
| Mouse monoclonal anti-HSP70 (1:1000) |
Santa Cruz |
Cat# sc-7298 |
| Mouse monoclonal anti-HSP90 (1:1000) |
Santa Cruz |
Cat# sc-13119 |
| Rabbit monoclonal anti-β-actin (1:1000) |
Cell Signaling |
Cat# 4970 |
| Rabbit polyclonal anti-cleaved Caspase-3 (1:500) |
Cell Signaling |
Cat# 9661 |
| Chicken polyclonal anti-GFP (1:1000) |
Aves Labs |
Cat# GFP-1020 |
| Rabbit polyclonal anti-RBM3 (1:1000) |
Proteintech |
Cat# 14363-1-AP |
| Rabbit polyclonal anti-CIRP (1:1000) |
Proteintech |
Cat# 10209-2-AP |
| Chemicals, Peptides, and Recombinant Proteins |
| Cell Culture Media Formulations & Reagents |
This paper |
N/A |
| B27 supplement minus insulin |
Thermo Fisher |
Cat# A1895601 |
| CHIR99021 |
Tocris |
Cat# 4423 |
| IWP4 |
Tocris |
Cat# 5214 |
| B27 supplement (complete) |
Thermo Fisher |
Cat# 17504044 |
| RPMI |
Thermo Fisher |
Cat# 11875093 |
| b-FGF |
R&D Systems |
Cat# 233-FB-025 |
| HGF |
R&D Systems |
Cat# 294-HG-005 |
| Hepatocyte Maintenance Media w/ Supplement |
Lonza |
Cat# MM250 |
| Oncostatin M |
R&D Systems |
Cat# 295-OM-010 |
| MG-132 (5 μM) |
Enzo Life Sci. |
Cat# ENZ-51035 |
| BAM15 (0.05-5 μM) |
Tocris |
Cat# 5737 |
| Protease inhibitor cocktail set III (PI) (1:500) |
Millipore |
Cat# 539134 |
| PYR-41 (5-10 μM) |
Tocris |
Cat# 2978 |
| Taxol (0.1 or 10 μM) |
Tocris |
Cat# 1097 |
| CellROX Green (1 μM) |
Thermo Fisher |
Cat# C10444
|
| TMRE (50 nM) |
Thermo Fisher |
Cat# T669 |
| Ames’ medium |
Sigma |
Cat# A1420 |
| TRIzol |
Thermo Fisher |
Cat#15596018 |
| LysoTracker Green DND-26 |
Thermo Fisher |
Cat# L7526 |
| RIPA lysis and extraction buffer |
Thermo Fisher |
Cat# 89900 |
| SYBR Green PCR Master mix |
Thermo Fisher |
Cat# 4309155 |
| BrightGreen Express 2X qPCR MasterMix-ROX |
ABM |
Cat# MasterMix-ER |
| Critical Commercial Assays |
| CytoTune iPS 2.0 Sendai Reprogramming Kit |
Thermo Fisher |
Cat# A16517 |
| Protein Oxidation Detection Kit |
Millipore |
Cat# S7150 |
| Proteostat Aggresome Detection Kit |
Enzo Life Sci. |
Cat# ENZ-51035 |
| LipoJet in vitro transfection kit |
SignaGen Laboratories |
Cat# SL100468 |
| RNeasy kit |
Qiagen |
Cat# 74104 |
| TruSeq® Stranded mRNA LT - Set A |
Illumina |
Cat# RS-122-2101 |
| NextSeq® 500/550 High Output Kit v2 |
Illumina |
Cat# FC-404-2002 |
| Magic Red cathepsin B assay kit |
Immuno-Chemistry Tech. |
Cat# 938 |
| Click-iT lipid peroxidation imaging kit – Alexa Fluor 488 |
Thermo Fisher |
Cat# C10446
|
| Deposited Data |
| RNA-seq Data |
This paper |
GEO: GSE93935
|
| Experimental Models: Cell Lines |
| Ground Squirrel iPSC line (female) |
This paper |
GS-iPSC1 |
| Ground Squirrel iPSC line (female) |
This paper |
GS-iPSC3 |
| Ground Squirrel Cortical primary cultures (male/female) |
This paper |
N/A |
| Human iPSC line (female) |
NIH NINDS Stem Cell Unit |
SCU-i10 |
| Human iPSC line (male) |
NIH NINDS Stem Cell Unit |
SCU-i19 |
| Human iPSC line (male) |
NIH NINDS Stem Cell Unit |
SCU-i21 |
| Experimental Models: Organisms/Strains |
| Thirteen-lined ground squirrel |
University of Wisconsin Oshkosh |
N/A |
| Sprague Dawley Rats (males and females) |
Charles River |
RRID: RGD_737891 |
| Mouse: Wild-type C57BL/6 (males and females) |
Jackson Labs |
RRID: IMSR_JAX:000664 |
| Recombinant DNA |
| pCMV6-XL5-TUBB3
|
Origene |
Cat# SC116313 |
| pCMV6-Myc-DDK-Tubb3
|
Origene |
Cat# MR207181 |
| pCMV6-UCP1-IRES2-eGFP
|
GeneCopoeia |
Cat# C0618-M61 |
| pCMV6-UCP2-IRES2-eGFP
|
GeneCopoeia |
Cat# M0658-M61 |
| Software and Algorithms |
| Matlab rev.2015a |
Mathworks |
https://www.mathworks.com/ |
| JMP |
SAS |
https://www.jmp.com/en_us/home.html |
| MC Rack |
MultiChannel Systems |
https://www.multichannelsystems.com/software/mc-rack |
| Plexon Offline Sorter v.3.3.5 |
Plexon Inc. |
https://plexon.com/products/offline-sorter/ |
| ImageJ Gel Analysis tool |
NIH |
https://imagej.nih.gov/ij/ |
| Image J (Simple Neurite Tracer plugin) |
(Longair et al., 2011) |
https://imagej.net/Simple_Neurite_Tracer |
| Bcl2fastq Conversion Software v2.19.1 |
Illumina |
https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-19.html |
| TopHat v2.1.1 |
(Trapnell et al., 2009) |
https://ccb.jhu.edu/software/tophat/index.shtml |
| R Subread Package |
(Liao et al., 2013) |
http://bioconductor.org/packages/release/bioc/html/Rsubread.html |
| DESeq2 |
(Love et al., 2014) |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Ensembl database (spetri2) |
(Yates et al., 2016) |
https://useast.ensembl.org/index.html |
| CLUSTAL Omega |
(McWilliam et al., 2013) |
https://www.ebi.ac.uk/Tools/msa/clustalo/ |
| NetAcet 1.0 Server |
(Kiemer et al., 2005) |
http://www.cbs.dtu.dk/services/NetAcet/ |
| ASEB |
(Wang et al., 2012) |
https://bioconductor.statistik.tu-dortmund.de/packages/2.12/bioc/html/ASEB.html |
| R Package piano |
(Varemo et al., 2013) |
https://bioconductor.org/packages/release/bioc/html/piano.html |
| R Package ggplot2 |
(Wickham, 2009) |
https://cran.r-project.org/web/packages/ggplot2/index.html |
