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3 protocols using gfp 2956

1

Mitochondrial Stress Response Modulators

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Compounds were used at the following concentrations unless otherwise noted: 50 μM AZD3988 (Tocris), 30 μM A922500 (Stratech), 50 μM AZD7687 (Stratech), 70 μM T863 (Sigma), 1 μM Oligomycin (Sigma), 0.5 μM FCCP (Sigma), 1 μM Antimycin-A (Sigma), 1 μM Rotenone (Sigma), 50 μM PF-06424439 (Sigma), 5 μM Ebselen (Tocris), 1 mM Tempol, 200 μM Paraquat (Sigma), Menadione (Sigma), 100 μM Etomoxir (Sigma), 2 μM Ferrostatin-1 (Sigma), 5 μM ML385 (Selleckchem), and 1 μM ATN-224 (Cayman Chemical). Antibodies against DGAT1 (ab54037) and 4-Hydroxynonenal (ab46545) were purchased from abcam. Antibodies against Vinculin (66305-1-Ig), Beta-Tubulin (10094-1-AP), PINK1 (23274-1-AP), Parkin (14060-1-AP), SOD1 (10269-1-AP), SOD2 (24127-1-AP), SESN2 (10795-1-AP) and GAPDH (60004-1-Ig) were purchased from Proteintech. Antibodies against phospho-AMPK (50081), phospho-RAPTOR (2083), Caspase-3 (9662), phospho-ERK (4370) and GFP (2956) were purchased from Cell Signalling. The antibody against gamma-tubulin (T5326) was purchased from Sigma. The antibody against ERK2 (C-14) was from Santa Cruz Biotechnology.
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2

Comprehensive Protein Analysis Protocol

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Total protein was extracted with RIPA lysis buffer, containing 25 mM Tris-HCl (pH 7.6), 150 mM NaCl, 1% Nonidet P-40, 1% sodium deoxycholate, 0.1% SDS, complete protease inhibitor, phosphatase inhibitor. Protein lysates were resolved on Bis-Tris gels, transferred to PVDF membranes, probed with primary antibodies overnight at 4 °C and then with HRP-linked secondary antibodies (GE Healthcare, IL) and visualized with ECL reagent (Thermo Fisher Scientific, MA). The following antibodies were used:
AntibodyCat. NoSourceWorking dilution
HA3724Cell Signaling Technology1:2000
Ago22897Cell Signaling Technology1:1000
Caveolin-13267Cell Signaling Technology1:1000
Acetylated lysine9441Cell Signaling Technology1:1000
DDK(Flag)GTX11043GeneTex1:1000
EEA12411Cell Signaling Technology1:1000
CalreticulinGTX111627GeneTex1:1000
HisA00186-100Genescript1:2000
Sirt19475Cell Signaling Technology1:1000
Sirt2GTX129154GeneTex1:1000
HDAC6GTX100722GeneTex1:1000
HDAC106-720Milipore1:1000
GFP2956Cell Signaling Technology1:2000
FibronectinBD610078BD Biosciences1:1000
N-cadherin13116Cell Signaling Technology1:1000
Dicer5362Cell Signaling Technology1:1000
GW182SC374458SantaCruz1:500
GAPDHGTX100118GeneTex1:5000
α-tubulinTA307175Origene1:5000
Integrin β1303010Biolegend1:250
CD81GTX101766GeneTex1:1000
CD63GTX135220GeneTex1:1000
AlixGTX135282GeneTex1:1000
TSG101GTX118736GeneTex1:1000
CD9GTX100912GeneTex1:1000
Apo-A1GTX12692GeneTex1:1000
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3

Immunostaining of Skeletal Muscle Samples

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Mouse skeletal muscles were removed as indicated in Results, put in OCT, frozen in dry ice-cooled isopentane (Tissue-Tek), fixed in 4% paraformaldehyde, and blocked in 3% BSA in Tris-buffered saline (TBS). C2C12 cells were fixed in 4% paraformaldehyde and blocked in 3% BSA in PBS. Samples were immunostained overnight with antibodies: AUF1 (07-260, Millipore), Slow myosin (NOQ7.5.4D, Sigma), Fast myosin (MY-32, Sigma), Laminin alpha 2 (4H8-2, Sigma), GFP (2956, Cell Signaling), and Myf5 (clone AF 4027; R&D Systems). Anti myosin type I (BA-D5), IIa (SC-71, and IIb (BF-F3) were from Developmental Studies Hybridoma Bank. Slow and Fast myosin staining was done with the MOM Kit (Vector Labs). Alexa Fluor donkey 488, 555, anti-mouse IgG2b 594 (type I), anti-mouse IgG1 488 (IIa), and anti-mouse IgM 647 (IIb) were from Thermo Fisher Scientific. Secondary antibodies were used at 1:300 and incubated for 1 h at room temperature. Slides were sealed with Vectashield with DAPI (Vector).
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