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8 protocols using mouse anti rab11

1

Visualizing Endocytic Recycling in Drosophila Pupae

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To analyze pupal eyes for endocytic recycling, we used the following Drosophila genotypes: (a) GMR-gal4/+; UAS-YFP-Rab5/+ and (b) GMR-gal4/+; UAS-YFP-Rab5/UAS-Rho1 RNAi. The 39-h after puparium formation (APF) pupal eyes were dissected in ice-cold S2 medium, incubated in rat anti–DE-cadherin antibody for 20 min on ice, washed, and transferred to 25°C for 2 h in S2 medium to allow endocytosis to occur. Eyes were washed in PBS at room temperature and fixed using the standard immunofluorescence protocol. The following antibodies were used for staining: rabbit anti-Rab5, rabbit anti-Rab11, and mouse anti-Rab11 (1:100; BD Transduction Laboratories, Lexington, KY). Confocal Z-stack slices were taken in 0.47-μm intervals of regions localizing DE-cadherin and quantitated vesicles present in each slice that were absent in the previous slice in order to avoid redundant counts. Images shown are of representative individual slices taken within the AJ region.
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2

Western Blot Analysis of Rab5 and Rab11 in Muscle

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Wildtype and EHD1-null quadriceps muscles were homogenized and 20μg of protein was separated on a 4–12% gel (Life Technologies). Protein was transferred to PDVF membrane and blocked with T-20 Starting Block (Pierce). Mouse polyclonal anti-Rab5 was used at 1:250 (BD Transduction Laboratories, 610281) and mouse anti Rab-11 was used at 1:250 (BD Transduction Laboratories, 610656). Secondary goat anti-mouse HRP was used at 1:2500. Images were acquired on a Bio Spectrum Imaging System (UVP) and processed in Adobe Photoshop.
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3

Antibody Sources and Immunostaining Protocols

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Antibodies were from the following sources: rat anti-Yl and rabbit anti-Yolk antibodies were from Dr. Mahowald [48 (link)]. mouse anti-Rab7 (1:10, Developmental Studies Hybridoma Bank (DSHB)), mouse anti-Rab11 (1:200, BD Transduction Laboratories (#610657)), mouse anti-actin (1:10000, MAB1501, Chemicon, and #ab-6276, Abcam); mouse anti-αTubulin (1:10000, DM1A, Sigma); mouse anti-HA (12CA5, Roche); chicken anti-GFP (Aves. 1:10,000 for Western blot and 1:2,000 for immunofluorescent staining). Alexa Fluor 488 AffiniPure Donkey Anti-Chicken IgY (1:1000, 703-545-155) and Rhodamine Red AffiniPure Donkey Anti-Mouse IgG (1:1000, 715-295-151) from Jackson ImmunoResearch Inc. TRITC-Phalloidin (Phalloidin–Tetramethylrhodamine B isothiocyanate) (1:200, P1951, Sigma). Alexa Fluor 488-Phalloidin (1:200, A-12379), Alexa Fluor 594-Phalloidin (1:200, A-12381), Alexa Fluor 647-Phalloidin (1:200, A-30107), Alexa Fluor 680-(A-21076) were from Molecular Probes (Invitrogen). Alexa Fluor 680-(A-21076) and Alexa Fluor 800-(926–32212) conjugated secondary antibodies for immunoblotting (1:10,000) were from Molecular Probes (Invitrogen) and LI-COR, respectively.
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4

Immunofluorescence and Immunoblotting Protocols

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The following primary antibodies
were used for immunofluorescence: mouse anti-LAMP1 (1/10.000) (H4A3
clone, Developmental Studies Hybridoma Bank), mouse anti-EEA1 (1/100)
(Transduction Laboratories, 610456), mouse anti-RAB11 (1/100) (BD
Transduction, 610,657). Donkey antimouse-AF647 (1/300) (Invitrogen
A32787) antibody was used as a secondary antibody. DAPI (Sigma, D9542)
at 0.1 μg/mL and HCS Cell Mask Blue Stain (1/400) (Invitrogen,
H32720) were used to mark nuclei and cytoplasm. The following tagged
transferrin was used: Tf-AF647 (1/1000) (Molecular Probes, T23366)
and Tf-488 (1/1000) (Molecular Probes).
The following primary
antibodies were used for immunoblotting: mouse anti-CHC (abcam ab2731)
(1/500), goat anti-DNM2 (Santa Cruz, SC-6400) (1/1000), and rabbit
anti-GAPDH (Sigma G9545) (1/6000). Goat antimouse-HRP (Amersham, NA931)
(1/10000), rabbit anti-goat-HRP (Biodesign, W99119P) (1/10,000), and
donkey antirabbit-HRP (Amersham, NA9340) (1/10000) were used as secondary
antibodies.
To measure cytotoxicity, the Cytotox96 Non-Radioactive
cytotoxicity
assay kit (Promega) measuring the extracellular LDH has been used
after a 6 h incubation at a concentration of 6 nM.
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5

Antibodies for ESCRT-II and Vesicular Trafficking

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Rabbit anti-Xenopus laevis ESCRT-II polyclonal antibody was made in the Blower laboratory; other antibodies were obtained as follows: mouse anti-acetylated α-tubulin (Sigma cat. no. T6793), mouse anti-α-tubulin (Sigma cat. no. T6074), mouse anti-Rab4 (BD Biosciences cat. no. 610888), mouse anti-Rab5 (BD Biosciences cat. no. 610281), mouse anti-Rab7 (Sigma cat. no. R8779), mouse anti-Rab11 (BD Biosciences cat. no. 610656), rabbit anti-β-tubulin (Abcam cat. no. ab6046), mouse anti-DCC intracellular domain (BD Biosciences cat. no. 554223), goat anti-DCC extracellular domain (R&D Systems cat. no. AF844), rabbit anti-RPL5 (Proteintech Europe cat. no. 15430-1-AP).
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6

Generating Antibodies for Zebrafish Studies

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Polyclonal antibodies to zebrafish Pacsin2 were generated in sheep by immunising with a recombinant GST-tagged Pacsin2 construct encoding amino acids 301-388. Immunisation and serum collection were by Orygen Antibodies Ltd. Antibodies were affinity purified from serum by first clearing on GST beads alone followed by affinity purification on the GST-Pacsin2 recombinant protein. Polyclonal antibodies to zebrafish megalin were generated in rabbits against a GST fusion to the cytoplasmic domain, and affinity purified on the recombinant protein. Also used in this study were goat anti-EEA1 (Santa Cruz Biotechnology, sc-6415), mouse anti-Rab11 (BD Transduction Labs, 610657), mouse 3G8 anti-proximal tubule (European Xenopus Resource Centre, Portsmouth, UK), and mouse anti-GAPDH (Santa Cruz Biotechnology, sc-25778). Fluorophore-and HRP-conjugated secondary antibodies were purchased from Thermo Fisher Scientific.
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7

Diverse Antibody Immunofluorescence Protocol

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Primary antibodies used were the following: mouse anti-Hts (1B1) (DSHB cat. no. 1b1, RRID:AB_528070), 1 : 100; rabbit anti-Vasa (a gift from R. Lehmann), 1 : 3000; goat anti-GFP, FITC conjugated (Abcam cat. no. ab6662, RRID:AB_305635), 1 : 500; alpaca anti-GFP-Booster_Atto488 (ChromoTek cat. no. gba488-100, RRID:AB_2631386), 1 : 200; mouse anti–Lamin C (DSHB cat. no. lc28.26, RRID:AB_528339), 1 : 30; rat anti-DE-cadherin (DSHB cat. no. DCAD2, RRID:AB_528120), 1 : 50; guinea pig anti-Hh (this work; raised against a His-tagged fragment of the Hh protein (aa. 82-257) produced in Escherichia coli; polyclonal antibodies were affinity purified), 1 : 100; rabbit anti-phospho-Mad (Abcam cat. no. ab52903, RRID:AB_882596), 1 : 1000; rabbit anti-cleaved Dcp-1 (Cell Signaling Technology cat. no. 9578, RRID:AB_2721060), 1 : 100; guinea pig anti-Nuf [33 (link)], 1 : 500; mouse anti-Rab11 (BD Biosciences cat. no. 610657, RRID:AB_397984), 1 : 100; mouse anti-Patched (DSHB cat. no. Drosophila Ptc (Apa 1), RRID:AB_528441), 1/100. DNA dye: Hoechst (Sigma B2883 10 mg ml−1 in H2O).
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8

Visualizing T-Cell Receptor and Actin Dynamics

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T cells (Jurkat or SAg‐T blasts) alone or in conjugates with Raji cells were seeded onto coverslips precoated with poly‐L‐lysine (Sigma) prior to fixation with 4% PFA for 10 min at RT. After three washings with PBS, the coverslips were then incubated with NH4Cl for 10 min to remove residual PFA. TCR and F‐actin were stained with anti‐CD3 Ab (clone UCHT1, Biolegend) and Phalloidin AF647 (ThermoFisher, A22287), respectively, followed by staining with secondary antibodies for 45 min at RT. Depending on the Abs, several protocols were used for intracellular staining. For mouse anti‐human Lck, permeabilisation with PBS supplemented with 0.05% saponin was performed for 15 min at RT, followed by incubation with the Ab diluted in the same buffer for 1 hr. For rabbit‐anti human‐GM130 (Abcam, ab52649) and mouse‐anti‐Rab11 (BD Bioscience, 610,657), permeabilisation was done with PBS supplemented with 0.1% Triton. Confocal microscopy was performed on a SP5 (Leica) or on an Opterra (Bruker) using either a 63× objective or a 100× objective (NA 1.4). Z‐stack acquisitions of optical sections were performed at 0.3 increments for analysis. Images were analysed using Fiji analysis software (Schindelin et al., 2012).
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