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2 protocols using oligomycin antimycin

1

Stem Cell and Retinal Ganglion Cell Maintenance

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hPSCs and RGCs were cultured and maintained on 1% (vol/vol) Matrigel-GFR (BD Biosciences) coated dishes in mTeSR and N2B27 media [34 (link)] respectively. Stem cells and RGCs were cultured in 37 °C hypoxia (10% CO2, 5% O2) and normoxia (5% CO2, 20% O2) incubators, respectively. The following drugs were used in this study: CCCP (Sigma), bafilomycin A1 (Baf, Sigma), hydroxychloroquine (HCQ, Fisher Scientific), bortezomib (Selleckchem), oligomycin (Millipore), antimycin (Sigma), oligomycin-antimycin (OA) drug combination used at 10 μM and 4 μM concentrations respectively, and MG132 (Sigma). All the drugs were dissolved in DMSO except hydroxychloroquine which is soluble in water and the stock solutions were prepared in a way such that each condition requires similar volume of drug solution. For hydroxychloroquine treatment similar volume of DMSO was added to the culture followed by drug addition. All the treatments were compared to the corresponding DMSO group.
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2

Identifying Conditions for K11/K48-linked Chain Formation

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To identify conditions of K11/K48-linked chain formation HEK 293T or HeLa cells were treated with different drugs: Epoxomycin (1µM, 6h, Sigma-Aldrich), MG132 (10µM, 6h, Sigma-Aldrich), Pifithrin µ (10µM, 6h, Sigma-Aldrich), VER155008 (40µM, 6h, Sigma-Aldrich), 17 DMAG (1µM, 6h, Sigma-Aldrich), Chloroquine (100µM, 6h, Abcam), DBEQ (10µM, 6h, Sigma-Aldrich), Oligomycin/Antimycin (each 10µM, 1h, Sigma-Aldrich), CCCP (10µM, 2h, Abcam), Cycloheximide (100µg/mL, 6h, Sigma-Aldrich), Puromycin (25µM, 1h, Sigma-Aldrich), DTT (2mM, 6h), Tunicamycin (10µg/mL, 2h, Sigma-Aldrich), Doxorubicin (5µM, 6h, Sigma-Aldrich). Translation and transcription inhibitors were used at the following concentrations: Cycloheximide (100µg/ml), Harringtonine (2µg/ml), Emetine (20µg/ml), Puromycin (1µg/ml), α- Amanitin (5µg/ml). Accumulation of K11/K48-linked chains was monitored by Western blot or immunofluorescence microscopy.
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