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2 protocols using pmp70

1

Antibodies and Inhibitors for Peroxisomal Proteome

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The antibodies used were as follows: TRIM37 (sc-515044; Santa Cruz Biotechnologies), ECH1 (sc-515270; Santa Cruz Biotechnologies), ACOT1/2 (sc-373917; Santa Cruz Biotechnologies), GSTK1 (sc-515580; Santa Cruz Biotechnologies), ubiquitin (sc-8017; Santa Cruz Biotechnologies), PMP70 (sc-514728; Santa Cruz Biotechnologies), LAMP1 (sc-20011; Santa Cruz Biotechnologies), VDAC1 (sc-390996; Santa Cruz Biotechnologies), Sec61-β (sc-393633; Santa Cruz Biotechnologies), PSMA2 (2455; Cell Signaling Technology), cleaved Caspase 3 (9664; Cell Signaling Technology), cleaved poly-ADP ribose polymerase (5625; Cell Signaling Technology), GAPDH (2118; Cell Signaling Technology), actin (A1978; Sigma-Aldrich), myc (C3956; Sigma-Aldrich), PEX14 (ab109999; Abcam), HA (11867423001; Roche), GFP (632593; Clontech), and histidine (34660; QIAGEN). Antibodies against PEX5 and PTS1 were previously described by Wiemer et al. (1995) (link). The inhibitors used were as follows: CHX (C104450; Sigma-Aldrich) and MG132 (C2211; Sigma-Aldrich). Components for in vitro ubiquitylation were purchased from Boston Biochem: UBE1 (E-305), E2 enzyme set (K-980B), and ubiquitin (U-100H). USP2 was provided by E. Bennett (University of California, San Diego).
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2

Quantifying Peroxisomes Using Immunostaining

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Immunostaining was carried out using the following antibodies: catalase (Cell Signaling Technology, Danvers, MA) and PMP70 (Santa Cruz Biotechnology, Inc., Dallas, TX). DAPI (Vector Laboratories, Burlingame, CA, USA) was used to counterstain the cell nuclei. Images were acquired with Zeiss LSM 710 confocal microscope (Zeiss International, Oberkochen, Germany). Fluorescence intensity was adjusted with ImageJ software (NIH). Quantitative measurement of peroxisomes number per square unit was performed using ImageJ. In each green-fluorescence channel image, cells of interest were outlined and their surface areas (in pixels) were measured. These outlined cells were then analyzed using the particle analysis function for the number of particles greater than 4 × 4 pixels, which indicated the PMP70-positive peroxisomes. To account for the size difference of the cells, the peroxisomes counts were normalized with the cell surface areas.
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