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10 protocols using sab4200181

1

Immunofluorescence Imaging of Lipid Droplets and Peroxisomes

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Cells were plated on coverslips (Marienfeld precision cover glasses 1.5 H) fixed in 4% paraformaldehyde for 10 min, and permeabilized with 0.5% TritonX-100 in PBS for 5 min. In the case of digitonin treatment to decrease cytosolic staining, cells were treated with PBS containing 0.01% digitonin for 5 min on ice, followed by fixation with 4% paraformaldehyde, as described previously45 (link). Fixed cells were incubated with primary antibodies against PLIN1 (20R-pp004; Fitzgerald Industries, 1:300), ATGL (2138S; Cell Signaling, 1:300), PMP70 (ab3421; Abcam, 1:300 (all fluorescence images of immunostained PMP70 except for Supplemetary Fig. 4d), SAB4200181; Sigma, 1:300 (fluorescence images of immunostained PMP70 for Supplementary Fig. 4d), PEX5 (ab125689; Abcam, 1:300 (fluorescence images of immunostained PMP70 for Fig. 6a), sc-23188; Santacruz, 1:200 (fluorescence images of immunostained PMP70 for Supplementary Fig. 4d)), Catalase (ab16771, Abcam, 1:300) overnight, washed three times for 5 min each, incubated in secondary antibody for 1–2 h, washed three times for 5 min each, and mounted on glass slides with mounting medium (Vectashield without DAPI; Vector Laboratories). Cells were observed and imaged using an LSM 700 confocal microscope, and an OMX SIM microscope.
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2

Mitochondrial and Autophagy Pathway Analysis

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Antibodies and other reagents used were as follows: anti-BNIP3L (#12396, 1:1,000 WB, 1:250 IF; Cell Signalling), anti-BNIP3 (ab109362, 1:1,000 WB; Abcam), anti-TOM20 (11802-1-AP, 1:1,000 WB; ProteinTech), anti-TOM20 (HPA011562, 1:500 IF; Sigma-Aldrich), anti-PMP70 (SAB4200181, 1:1,000 WB, 1:250 IF; Sigma-Aldrich), mouse anti‐actin (66009-1-Ig, 1:10,000; ProteinTech), anti-Cullin-2 (A302-476A, 1:2,000 WB; Bethyl Laboratories), anti-HIF1⍺ (NB100-134, 1:1,000; Novus Bio techne), anti-ATG7 (2631, 1:1,000 WB; Cell Signalling), anti-NBR1 (9891S, 1:1,000 WB; Cell Signalling), anti-LC3 (5F10, 1:200 WB; Nanotools), MLN4924 (C-1231; Chemgood), deferiprone (379409; Sigma-Aldrich), 4-PBA (21005; Sigma-Aldrich), clofibrate (C6643; Sigma-Aldrich), hydrogen peroxide (H1009; Sigma-Aldrich), oligomycin A (75351; Sigma-Aldrich), antimycin A (A8674; Sigma-Aldrich), Mitotracker Deep Red FM (M22426; Invitrogen).
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3

Immunofluorescence Labeling of Peroxisomes

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Fixed cells were quenched with 50 mM NH4Cl for 10 min, permeabilized with 0.1% saponin (Sigma S4521) in PBS for 10 min, and blocked by incubation with 10% FBS in PBS for 30 min. The cells were then stained with anti-PMP70 antibodies (Sigma, SAB4200181) for 1 h and Alexa Fluor 568-conjugated secondary antibodies (Thermo Fisher, A11004) for 30 min. Prior to each antibody incubation, the cells were washed with 0.1% saponin in PBS. Cells mounted with Mowiol/DABCO (Calbiochem 475904/Sigma D2522) were imaged with a confocal Leica Stellaris 8 inverted microscope using × 63 HC PL APO CS2 oil objective NA 1.40.
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4

Immunoblotting Antibody Detection Protocol

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Detecting reagents, including streptavidin-HRP (1:2,000 for WB, 3999S), anti-Myc antibody (1:2,000 for WB, 2276S), anti-Myc HRP (1:1,000 for WB, 2040S), anti-HA antibody (1:2,000 for WB, 2367S), anti-HA HRP (1:1,000 for WB, 2999S), V5 (1:1,000 for immunofluorescence, 13202S), and anti-GFP HRP (1:1,000 for WB, 2037S) were purchased from Cell Signaling Technology. Antibodies against V5 (1:3,000 for WB, ab27671) and MARCH5 (1:2,000 for WB, ab174959) were purchased from Abcam. Anti-GDAPH (1:4,000 for WB, A00191) and anti–β-actin (1:4,000 for WB, A00702) were purchased from GenScript. Other antibodies used in this study included anti-FLAG (1:2,000 for WB, GNI14110-FG) and anti-FLAG HRP (GNI4310-FG; GNI), anti-PMP70 (1:3,000 for WB, SAB4200181; Sigma-Aldrich), and anti-GFP (1:3,000 for WB, M20004; Abmart). Anti–V5-HRP (1:5,000 for WB, R961-25) was purchased from Thermo Fisher Scientific. Other primary antibodies used were anti-MARCH5 (19168S; Cell Signaling Technology), anti-PEX19 (14713–1-AP; Proteintech), anti-PEX3 (sc-271477; Santa Cruz Biotechnology), anti-catalase (219010; Millipore), and anti-PEX13 (ab235043; Abcam). Secondary antibodies conjugated to HRP were purchased from GenScript.
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5

Antibodies for ACBD5, PEX14, VAPB Immunoblotting

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PLA: Anti-ACBD5 rabbit antibody (HPA012145; Sigma-Aldrich), anti-PEX14 rabbit antibody (Grant et al., 2013 (link)) (generated by D. Crane, Griffith University, Brisbane, Australia) and anti-VAPB mouse antibody (66191-1-Ig; Proteintech) were used. Immunoblots: Anti-ACBD5, PEX14 and VAPB as above, Anti PMP70 (SAB4200181; Sigma) Anti-PEX11β (ab 182100; Abcam), Anti-Catalase (ab179843; Abcam), Anti-GAPDH (ProSci).
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6

Antibody Panel for Peroxisomal Protein Detection

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Rabbit FLAG antibody (#14793, Cell Signaling Technology), mouse CAT antibody (YIF-LF-MA0003, Biomol International), mouse GAPDH antibody (AM4300, Invitrogen), rabbit PGD antibody (#13389, Cell Signaling Technology), rabbit TKT antibody (#8616, Cell Signaling Technology), rabbit NRF2 antibody (#12721, Cell Signaling Technology), rabbit CAT antibody (ab16731, Abcam), rabbit PMP70 antibody (ab3421, Abcam), rabbit PEX12 antibody (ab103456, Abcam), rabbit PGLS antibody (ab127560, Abcam), rabbit β-actin antibody (ab8227, Abcam), rabbit IREB2 antibody (ab181153, Abcam), mouse PMP70 antibodies (SAB4200181, Sigma). Rabbit antibodies to PEX5 (Otera et al., 2000 (link)), PEX13 (Mukai and Fujiki, 2006 (link)), PEX14 (Shimizu et al., 1999 ), ACOX1 (Tsukamoto et al., 1990 (link)), LONP2 (Okumoto et al., 2011 ) were used as described in corresponding references.
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7

Protein Detection Reagents for Western Blotting and Immunofluorescence

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Detecting reagents used for western blotting include: streptavidin-HRP (Cell Signaling, 3999S, 1:3000), anti-Myc (Cell Signaling, 2276S, 1:3000), anti-V5 (Abcam, ab27671, 1:3000), anti-β actin (GenScript, A00702, 1:3,000), anti-FLAG (GNI, GNI14110-FG, 1:3000), anti-ABCD3 (Sigma, P0497, 1:3000), anti-MFN1 (Cell Signaling, D6E2S, 1:3000), anti-MFN2 (Cell Signaling, D1E9, 1:3000). Antibodies used for immunofluorescence include: anti-MFN1 (Cell Signaling, D6E2S, 1:500), anti-MFN2 (Cell Signaling, D1E9, 1:500), anti-calnexin (Abcam, ab22595, 1:500), anti-EEA1 (Cell Signaling, C45B10, 1:500), anti-GM130 (Abcam, ab52649, 1:500), anti-LAMP1 (Cell Signaling, D2D11, 1:500), anti-ABCD3 (Sigma, SAB4200181, 1:500), anti-ABCD3 (Sigma, P0497, 1:500), anti-catalase (Merck/Millipore, 219010, 1:500), anti-FLAG (GNI, GNI14110-FG, 1:500), anti-FLAG (Proteintech, 20543-1-AP, 1:500), anti-Myc (Cell Signaling, 2276S, 1:500), anti-COX4 (Proteintech, 11242-1-AP, 1:500).
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8

Immunoblotting and Blue Native PAGE Analysis

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Fibroblasts were lysed with ice-cold RIPA buffer (50 mM Tris-Cl, pH 8.0, 150 mM NaCl, 1% Nonidet P-40, 0.1% sodium dodecyl sulfate, 0.5% sodium deoxycholate, protease inhibitors, and phosphatase inhibitors). The samples were separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (PAGE) and transferred to a PVDF membrane (Bio-Rad, Hercules, CA). Membranes were blocked with 5% non-fat milk and then incubated with anti-HSD17B4 (1:250, HPA021302; Atlas Antibodies, Stockholm, Sweden), anti-PMP70 (1:500, SAB4200181; Sigma-Aldrich, St. Louis, MO), anti-ß-actin (1:2000, sc-47778; Santa Cruz Biotechnology, Dallas, TX), and anti-α tubulin (1:25000, 11224-1-AP; Proteintech, Rosemont, IL) primary antibodies. The immunoreactive bands were detected with LAS-4000 (GE Healthcare, Chicago, IL). The quantitative densitometric analyses were performed with Image Quant LAS 4000 software (GE Health care). Blue native PAGE (BN-PAGE) analysis was performed using the NativePAGE Novex Bis-Tris Gel System (Life Technologies, Carlsbad, CA). We used the NativePAGE 4–16% Bis-Tris Protein Gel (Life Technologies). Fibroblasts were lysed with ice-cold lysis buffer (50 mM bis-tris [HCl], pH 7.2, 50 mM NaCl, 10% glycerol, 0.001% Ponceau S, 1% digitonin, protease inhibitors, and phosphatase inhibitors).
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9

Immunofluorescence Imaging of Fibroblasts

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Fibroblasts were fixed with 4% paraformaldehyde and stained with anti-HSD17B4 (1:50, HPA021302; Atlas Antibodies) and anti-PMP70 (1:250, SAB4200181; Sigma-Aldrich) antibodies. Anti-rabbit IgG Alexa Fluor 594 and anti-mouse IgG Alexa Fluor 488 (1:500; Thermo Fisher Scientific) were used as secondary antibodies. Immunostained cells were examined using a confocal microscope (LSM800; Carl Zeiss, Jena, Germany). Intensities were analyzed using ImageJ.
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10

Indirect Immunofluorescence Microscopy of Peroxisomes

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Cells were prepared for indirect IF as previously described,29 (link) mounted onto slides using ProLong Gold Antifade Reagent with DAPI (Invitrogen, Waltham, MA, USA), and visualized using a Leica DMI600 microscope with a DFC345FX camera and LASX software (Leica, Richmond Hill, ON, Canada). Primary antibodies used were 1:300 rabbit anti-PTS1 (generated and gifted by Dr. Steven Gould, Johns Hopkins University, Baltimore, MD, USA), 1:150 mouse anti-human ABCD3 (SAB4200181; Sigma-Aldrich, St. Louis, MO, USA), and 1:300 rabbit anti-HsPEX5 (generated and gifted by Dr. Gabriele Dodt, University of Tübingen, Germany). Secondary antibodies used were 1:400 Alexa Fluor 488 anti-rabbit (A21206; Invitrogen, Waltham, MA, USA) and 1:300 Alexa Fluor 594 anti-mouse (A11005; Invitrogen, Waltham, MA, USA).
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