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4 protocols using anti rab7 d95f2

1

Endosomal Trafficking Lipid Composition

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DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine), bovine liver phosphatidylinositol (PI), brain PS, and egg PA were purchased from Avanti Polar Lipids. PI 3-phosphate diC16 [PI(3)P], PI 4-phosphate diC16 [PI(4)P], and PI 5-phosphate diC16 [PI(5)P] were obtained from Echelon Biosciences. Folch fraction I and egg PC were purchased from Sigma-Aldrich. YM201636 PIKfyve inhibitor was purchased from Cayman Chemical. A cell fractionation kit was obtained from Cell Signaling Technology. Nontargeting control siRNA was obtained from Horizon Discovery, and human KLC1/2 siRNAs were from Santa Cruz Biotechnology. The following primary antibodies were used: horseradish peroxidase (HRP)–conjugated anti-His6 (71841, Novagen), anti-GFP for immunoblotting (3E1, Roche), anti-actin (AC-74, Sigma-Aldrich), anti–β-tubulin (AA2, Sigma-Aldrich), anti–histone H3 (Abcam), anti-giantin (PRB-114C, Covance), anti-HA (HA-7, Sigma-Aldrich), anti-KLC1 ([EPR12441(B)], Abcam), anti-KLC2 (Abcam), anti-KIF5B (Abcam), anti-LAMP1 (lysosome-associated membrane protein 1) (D2D11, Cell Signaling Technology), anti-Rab7 (D95F2, Cell Signaling Technology), and anti-Rab6 (D37C7, Cell Signaling Technology). Alexa 568– and Alexa 633–conjugated anti-mouse or anti-rabbit secondary antibodies were from Thermo Fisher Scientific.
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2

Antibody Validation for Western Blotting

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Primary antibodies used for Western blotting and immunofluorescent staining were as follows: anti–syntaxin 7 (AF5478; R&D Systems), VAMP8 (104302; Synaptic Systems, Goettingen, Germany), MPO (HM1051; Hycult Biotech, Uden, Netherlands), TLR9 (PA5-20203; Thermo Fisher Scientific, Asheville, NC), phosphorylated Erk and total Erk (9101, 9202; Cell Signaling Technology, Danvers, MA), phosphorylated P38 and total P38 (9211, 9212; Cell Signaling Technology), Flag (CGAB-DDK; Genecopoeia), GFP (A6455; Life Technologies, Carlsbad, CA), LAMP1 (sc-19992; Santa Cruz Biotechnology, Santa Cruz, CA), Myc (sc-40; Santa Cruz Biotechnology), Munc13-4 (described previously; Brzezinska et al., 2008 (link)), and anti-Rab7 (D95F2; Cell Signaling Technology).
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3

Immunofluorescence Imaging of Endosomal Markers

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Cells were grown to 70% confluence on glass coverslips, fixed for 20 minutes at room temperature in 4% paraformaldehyde, and blocked in 50mM ammonium chloride for 10 minutes and subsequently 0.1% bovine serum albumin in phosphate-buffered saline (PBS) for 20 minutes. Cells were incubated with primary antibodies anti-BMP/LBPA antibody clone 6C4 (MABT837, Millipore Sigma; 1/100), anti-LAMP1 (L1418, Sigma-Aldrich; 1:100) and anti-Rab7 D95F2 (9367, Cell Signaling; 1/100) in PBS containing 0.5% saponin for 30 minutes at room temperature. Following incubation with Alexa Fluor secondary antibodies (1:1000) for 30 minutes, cells were mounted in 4′,6-diamidino-2-phenylindole (DAPI) Fluoromount-G (0100–20, Southern Biotech). Samples were imaged with a Zeiss LSM 710 AxioObserver confocal microscope and analyzed with ZenBlue software.
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4

Immunofluorescent Characterization of Endocytic Organelles

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Cells were grown to 70% confluence on glass coverslips, fixed for 20 minutes at room temperature in 4% paraformaldehyde, and blocked in 50mM ammonium chloride for 10 minutes and subsequently 0.1% bovine serum albumin in phosphate-buffered saline (PBS) for 20 minutes. Cells were incubated with primary antibodies anti-BMP/LBPA antibody clone 6C4 (MABT837, Millipore Sigma; 1/100), anti-LAMP1 (L1418, Sigma-Aldrich; 1:100) and anti-Rab7 D95F2 (9367, Cell Signaling; 1/100) in PBS containing 0.5% saponin for 30 minutes at room temperature. Following incubation with Alexa Fluor secondary antibodies (1:1000) for 30 minutes, cells were mounted in 4′,6-diamidino-2-phenylindole (DAPI) Fluoromount-G (0100-20, Southern Biotech). Samples were imaged with a Zeiss LSM 710 AxioObserver confocal microscope and analyzed with ZenBlue software.
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