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. Author manuscript; available in PMC: 2021 Dec 9.
Published in final edited form as: Cell Rep. 2021 Nov 9;37(6):109965. doi: 10.1016/j.celrep.2021.109965

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Chemicals, peptides, and recombinant proteins
Anti-ALDH1A1 Invitrogen Cat#PA5-95937; RRID:AB_2807739
4-hydroxy-nonenal Cayman Chemical Company 32100
Malondialdehyde tetrabutylammonium salt Millipore Sigma 36357-100MG
All trans-Retinal, powder, ≥ 98% Sigma-Aldrich R2500-100MG
Ethanol Millipore-Sigma 1009831011
S-Trap mini columns (100 – 300 μg) Protifi CO2-mini-80
C 18 Tips Thermo Fisher Scientific 87784
Triethylammonium bicarbonate buffer Sigma-Aldrich T7408-500ML
DTT,1,4-Dithiothreitol Millipore-Sigma 11583786001
Iodoacetamide Sigma-Aldrich I1149-5G
Thermo Scientific Pierce MS Grade Trypsin Thermo Fisher Scientific 90058
β-Nicotinamide adenine dinucleotide sodium salt Sigma-Aldrich N0632-5G
Critical commercial assays
Cell Proliferation Reagent WST-1 Millipore-Sigma Cat.#5015944001
Deposited data
Proteomics This paper ProteomeXchang: PXD028546
RNA-Seq This paper NCBI: SRS6617922
RNA-Seq This paper NCBI: SRS6617923
RNA-Seq This paper NCBI: SRS6617924
RNA-Seq This paper NCBI: SRS6617925
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644691
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644699
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644707
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644715
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644723
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644690
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644698
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644706
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644714
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644722
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644695
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644703
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644711
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644719
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644727
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644694
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644702
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644710
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644718
RNA-Seq (Zhao et al., 2021) NCBI: SRX11644726
RNA-Seq This paper NCBI: SRR15970260
RNA-Seq This paper NCBI: SRR15970261
RNA-Seq This paper NCBI: SRR15970262
RNA-Seq This paper NCBI: SRR15970263
RNA-Seq This paper NCBI: SRR15970264
RNA-Seq This paper NCBI: SRR15970265
RNA-Seq This paper NCBI: SRR15970266
RNA-Seq This paper NCBI: SRR15970267
RNA-Seq This paper NCBI: SRR15970268
RNA-Seq This paper NCBI: SRR15970269
RNA-Seq This paper NCBI: SRR15970270
RNA-Seq This paper NCBI: SRR15970271
RNA-Seq This paper NCBI: SRR15970272
RNA-Seq This paper NCBI: SRR15970273
RNA-Seq This paper NCBI: SRR15970274
RNA-Seq This paper NCBI: SRR15970275
RNA-Seq This paper NCBI: SRR15970276
RNA-Seq This paper NCBI: SRR15970277
RNA-Seq This paper NCBI: SRR15970278
RNA-Seq This paper NCBI: SRR15970279
RNA-Seq This paper NCBI: SRR15970280
RNA-Seq This paper NCBI: SRR15970281
RNA-Seq This paper NCBI: SRR15970282
RNA-Seq This paper NCBI: SRR15970283
RNA-Seq This paper NCBI: SRR15970284
RNA-Seq This paper NCBI: SRR15970285
RNA-Seq This paper NCBI: SRR15970286
Software and algorithms
Trinity Haas et al., 2013 https://github.com/trinityrnaseq/trinityrnaseq/wiki
BUSCO Simão et al., 2015 https://busco.ezlab.org/
RepBase Bao et al., 2015 https://www.girinst.org/repbase/
RepeatMasker Tarailo-Graovac and Chen, 2009 https://www.repeatmasker.org/
Maker2 Holt and Yandell, 2011 https://www.yandell-lab.org/software/maker.html
MUSCLE Edgar, 2004 https://www.drive5.com/muscle/
RAxML Stamatakis, 2014 https://github.com/stamatak/standard-RAxML
PosiGene Sahm et al., 2017 https://github.com/gengit/PosiGene
OrthoDB Zdobnov et al., 2017 https://www.orthodb.org/v9/index.html
CAFÉ 3 Han et al., 2013 https://github.com/hahnlab/CAFE
GeneWise Birney et al., 2004 ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
DeSeq2 Love et al., 2014 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Kallisto Bray et al., 2016 https://pachterlab.github.io/kallisto/
SwissModel Waterhouse et al., 2018 https://swissmodel.expasy.org/
Experimental models: cell lines
Beaver/Mouse lung fibroblast cells This paper N/A