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5 protocols using ab125356

1

Immunoblotting, IP, and IF Antibody Protocols

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Primary antibodies against the following epitopes were used: flag (1:5,000 immunoblot, 1:200 immunoprecipitation; #F3165, Sigma‐Aldrich), GST (1:5,000; #sc‐138 Santa Cruz Biotechnology), PJA2 (1:1,000 immunoblot, 1:200 immunoprecipitation, 1:200 immunofluorescence; #A302‐991A, Bethyl Laboratories), GPR161 (1:100 immunofluorescence #13398‐1‐AP, Proteintech), SSTR3 (1:200 immunofluorescence #20696‐1‐AP, Proteintech), HA.11 (1:1,000; #16B12, BioLegend), mouse acetylated tubulin (1:600 immunofluorescence; #T7451, Sigma‐Aldrich), rabbit acetylated tubulin (1:600 immunofluorescence; #ab125356, Abcam), myc (1:1,000; #M4439, Sigma‐Aldrich; 1:800 immunofluorescence, Novus Biologicals #NB600‐335), ARL13B (1:500; #17711‐I‐AP, Proteintech). Antibody–antigen complexes were detected by HRP‐conjugated antibodies (Bio‐Rad Laboratories) and ECL (EuroClone). The following chemicals were used: Forskolin (40 μM; #F3917, Sigma‐Aldrich); Purmorphamine (10 μM; # ab120933 Abcam); somatostatin‐14 (10 μM; #38916–34‐6 Sigma‐Aldrich).
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2

Comprehensive Western Blot Analysis

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Western blot was performed as previously described 20 (link). Primary antibody used in our studies included Ac-α-Tub, collagen type I (COL I), KIF3A (ab125356, ab34710, ab11259, Abcam), intraflagellar transport protein (IFT) 88 (MFG42775, Aviva Systems Biology), ARL13B (GTX122703, GeneTex), α-SMA, (1184-1, Eptomics), MRTF-A, SHH, SMO, GLI1 (A12598, A7726, A3274, and A8387, ABclonal, Wuhan, China), SRF, PTC1, α-Tub (AF6160, AF5202, AF7010, Affinity Biosciences, Cincinnati, OH, USA), Ac-α-Tub, LaminB, GLI2, GLI3, and GAPDH (sc-23950, sc-56143, sc-271786, sc-74478, and sc-25778, Santa Cruz Biotechnology, Santa Cruz, CA, USA).The results were normalised with loading control and expressed as the fold of the specific bands to the control group. Western blotting was repeated at least three times.
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Immunohistochemistry Staining Protocol

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IHC staining was performed as previously described 20 (link) and with primary antibodies against α-SMA (1184-1, Eptomics, Burlingame, CA, USA, 1:300) and Ac-α-Tub (ab125356, Abcam, Cambridge, MA, USA, 1:300). Immunoreactivity was visualised with DAB (ZLI-9018, ZSGB-BIO, Beijing, China). Brown staining was considered a positive result.
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Quantitative Axon Fragmentation Imaging

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The cultures were fixed at specific time points using 4% paraformaldehyde in PBS. Stable microtubules in the axons were visualized using immunocytochemistry with an antibody against acetylated alpha-tubulin (Abcam, ab125356) and an Alexa Fluor 488-conjugated secondary antibody (Thermo Fisher, A-21206). Samples were immuno-stained and imaged under identical settings for quantitative analyses. The axon fragmentation index was defined as the proportion of the lost axonal length. Specifically, traces of axons in an image were manually delineated as segmented lines. The channel for acetylated alpha-tubulin was thresholded to generate a binary copy of the same image on which traces of axons were superimposed. Then axon fragmentation index for the entire image was calculated as [the sum of the lengths of axons not stained with acetylated alpha-tubulin] divided by [the sum of all axonal traces]. All experiments were performed with at least three independent biological replicates.
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5

Immunofluorescence Imaging of Embryonic Eye

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Fixed embryos were saturated with 30% sucrose in 1× PBS, cryo-sectioned in the coronal plane at the 12-µm thickness, and mounted on a slide glass. Antigen retrieval was performed in 10 mM sodium citrate with 0.05% Tween-20 (pH 6.0) at 95°C for 20 min. The slides were then blocked in 5% normal donkey serum in 1× PBS-T (0.05% Tween-20 in 1× PBS) for 30 min at room temperature and transferred to the blocking solution containing a rabbit anti-acetylated alpha tubulin antibody (1:300, ab125356; Abcam, UK). After incubating at 4°C for 16 h, the slides were washed three times with PBS-T, and the secondary antibody solution with an anti-rabbit IgG antibody conjugated to Alexa Fluor 555 (A-31572; Sigma) in PBS-T (1:1,000) was added. After incubating at room temperature for 1 h, the slides were washed three times with PBS-T, and nuclei were counterstained with Hoechst 33342 (Sigma) dissolved in 1× PBS (1:20,000). The slides were mounted in FluorSave (Sigma) with a cover glass. Five embryos were randomly chosen per group, and three coronal tissue sections around the longest axis of the eye were selected per embryo for cell counting in Fig. 3.
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