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5 protocols using rabbit anti rab7

1

Immunofluorescence and Immunoblot Analyses

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The following primary antibodies and dilutions were used for immunofluorescence
studies: mouse anti-Flag (Sigma-Aldrich, F3165) (1:1000), rabbit anti-TOM20 (Santa-Cruz,
sc11415) (1:1000), rabbit anti-PMP70 (Sigma-Aldrich, SAB4200181) (1:1000), mouse
anti-p230 (BD Biosciences, 611281) (1:1000), rabbit anti-Rab7 (Abcam, ab137029)
(1:1000), rat anti-Calnexin (Biolegend, 699401) (1:1000) and mouse anti-Neurofilament H
(Biolegend, 835801). Donkey anti-mouse, Goat anti-mouse IgG1, Goat anti-mouse IgG2a,
Goat anti-rabbit and Goat anti-rat, Alexa Fluor 488, 568 or 647 were used as secondary
antibodies (1:1000) (Invitrogen).
The following primary antibodies and dilutions were used for immunoblot analysis: mouse
anti-Flag (Sigma-Aldrich, F3165) (1:1000), mouse anti-VDAC1 (Abcam, ab14734) (1:1000),
rabbit anti-TMEM63C (Abcam, ab203486) (1:500), rabbit anti-Pex14 (Proteintech,
10594-1-AP) (1:1000), rabbit anti-Calnexin (Proteintech, 10427-1-AP) (1:1000), mouse
anti-Tubulin (Santa-Cruz, sc23948) (1:1000), rabbit anti-VAPB (Atlas, HPA013144) (1:500)
and mouse anti-ACSL4 (Santa-Cruz, sc-365230) (1:1000). Horseradish peroxidase-conjugated
anti-rabbit and anti-mouse IgG (GE Healthcare) were used as secondary antibodies
(1:3000).
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2

Immunostaining and Western Blot Protocols

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For immunostaining, primary antibodies used were mouse anti-RSV N (Abcam, Cat. No. ab22501), mouse anti-RSV G (Abcam, Cat. No. ab94966), rabbit anti-camelid VHH (GenScript, Cat. No. A01860-200), goat anti-panRSV polyclonal (Millipore, Cat. No. AB1128), rat anti-CD63 (BD, Cat. No. 564221), rabbit anti-Rab5 (Affinity BioReagents, Cat. No. PA3-915), and rabbit anti-Rab7 (Abcam, Cat. No. 137029). All primary antibodies for immunostaining experiments were used at 1 µg/mL. Secondary antibodies used were donkey anti-human Alexa Fluor 647 (Jackson ImmunoResearch), donkey anti-goat Alexa Fluor 546, donkey anti-rabbit Alexa Fluor 488, and donkey anti-mouse Alexa Fluor 488 (all from Life Technologies). All secondary antibodies for immunostaining experiments were used at 4 µg/mL. For dSTORM experiments, secondary antibodies used were donkey anti-mouse Alexa Fluor 647 (Life Technologies) and goat anti-human CF568 (Biotium), and both were used at 1 µg/mL.
For western blot, the primary antibodies used were a rabbit monoclonal anti phosphorylated eIF2α (Cell Signaling Technologies, Cat. No. 9721) and goat anti-pan-eIF2α (R&D Systems, Cat. No. AF3997) diluted 1:1000 in 5% BSA in TBS with 0.1% Tween-20. The secondary antibodies were a donkey anti-mouse IRDye 680RD (LI-COR) and a donkey anti-rabbit IRDye 800 (LI-COR) and were diluted 1:5000 in 5% BSA in TBS with 0.1% Tween-20.
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Purification and Analysis of Latex Bead Phagosomes

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Late phagosomes were purified from J774E cells 10 min/20 min (pulse/chase) after phagocytosis of 2 μm latex beads as described for LBPs containing 1 μm latex beads above. Purified LBPs were incubated for 30 min at 37°C with 10 μM hexahistidine-tagged Arl8b(Q75L) or Arl8b(T34N), in HB containing an ATP-regenerating system, 1x salts, and 1 mM DTT.33 (link) LBPs were isolated from reaction mixtures by density gradient centrifugation and fixed onto glass coverslips. Samples were sequentially incubated with PBS/50 mM NH4Cl and with blocking buffer (PBS/4% goat serum) for each 15 min at ambient temperature. LBPs were incubated with a mouse anti-Histidine tag antibody (1:50 in blocking buffer) for 60 min, washed five times with PBS, and incubated with an Alexa 535-conjugated goat anti-mouse antibody (1:200, blocking buffer). Samples were washed five times with PBS and incubated with rabbit anti-Rab2 or rabbit anti-Rab7 (Abcam) antibodies (each 1:50, blocking buffer) for 60 min at ambient temperature. Samples were washed five times with PBS and incubated with an Alexa 488-labeled goat anti-rabbit antibody (30 min, 1:200 in blocking buffer). Samples were washed four times with PBS, twice with ddH2O and mounted in Mowiol. Samples were analyzed using a Zeiss Axio Imager equipped with Apotome and a 100x oil immersion lens.
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4

Purification and Analysis of Latex Bead Phagosomes

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Late phagosomes were purified from J774E cells 10 min/20 min (pulse/chase) after phagocytosis of 2 μm latex beads as described for LBPs containing 1 μm latex beads above. Purified LBPs were incubated for 30 min at 37°C with 10 μM hexahistidine-tagged Arl8b(Q75L) or Arl8b(T34N), in HB containing an ATP-regenerating system, 1x salts, and 1 mM DTT.33 (link) LBPs were isolated from reaction mixtures by density gradient centrifugation and fixed onto glass coverslips. Samples were sequentially incubated with PBS/50 mM NH4Cl and with blocking buffer (PBS/4% goat serum) for each 15 min at ambient temperature. LBPs were incubated with a mouse anti-Histidine tag antibody (1:50 in blocking buffer) for 60 min, washed five times with PBS, and incubated with an Alexa 535-conjugated goat anti-mouse antibody (1:200, blocking buffer). Samples were washed five times with PBS and incubated with rabbit anti-Rab2 or rabbit anti-Rab7 (Abcam) antibodies (each 1:50, blocking buffer) for 60 min at ambient temperature. Samples were washed five times with PBS and incubated with an Alexa 488-labeled goat anti-rabbit antibody (30 min, 1:200 in blocking buffer). Samples were washed four times with PBS, twice with ddH2O and mounted in Mowiol. Samples were analyzed using a Zeiss Axio Imager equipped with Apotome and a 100x oil immersion lens.
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5

Intracellular Trafficking in Listeria Infection

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BMDM cells were infected with CFSE-labeled L.monocytogenes, Δhly, or incubated with NP and fixed at indicated times. After fixation, cells were permeabilized with 0.2% Triton X-100 (Sigma Aldrich) for 5 min at RT. Cells were washed with nuclease free PBS and blocked with 5% BSA in PBS for 30 min at 37 °C. Next, cells were incubated for 30 min at 37 °C with primary antibodies (Ab) diluted in PBS. Primary Abs used were mouse anti-clathrin light chain (1:500, Biolegend, Cat. No. MMS-423P), rabbit anti-caveolin-1 (1:200, Santa Cruz, Cat. No. sc-894), and rabbit anti-Rab7 (1:100, Abcam, Cat. No. ab137029). Rabbit anti-p-p38 (1:200, CellSignaling, #9211). Cells were then washed with PBS and incubated for 30 min at 37 °C with secondary Abs. Secondary Abs used were donkey anti-mouse conjugated to Alexa Fluor 546 (Thermo Fisher) or donkey anti-rabbit conjugated to Alexa Fluor 647 (Thermo Fisher). Goat anti-rabbit IgG Alexa-Flour-549. Finally, cells were washed with PBS and stained with DAPI for 5 min. Glass coverslips were mounted onto stained cells using Prolong Gold (Thermo Fisher).
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