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6 protocols using rpn1231

1

Rapid Transcriptional Profiling in RPE1 Cells

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RPE1 cells were seeded in a six-well plate (Techno Plastic Products, 92406; 100,000 cells/well) and treated with 1 μg/ml dox for 4 days. Medium was aspirated and replaced with medium containing 1 mM 4SU (Sigma, T4509). Actinomycin D (1 μg/ml) (Thermo Fisher Scientific, 11805017) was used as a negative control and was added at the moment of 4SU labeling. RNA was harvested using the RNeasy Mini kit (Qiagen) 20 or 120 min after 4SU labeling. Newly synthesized RNA (10 μg) was biotinylated using MTSEA biotin-XX linker (Biotium, BT90066), purified, dot-blotted on Hybond-N membrane (Amersham) and probed with streptavidin-horseradish peroxidase (RPN1231, Cytiva) as described previously (Gregersen et al., 2020 (link)).
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2

Western Blot Analysis of Tagged Proteins

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Total leaf proteins were extracted in SDS sample buffer and separated by SDS-PAGE as described previously [45 (link)]. Proteins were transferred onto a nitrocellulose membrane and probed with specific antibodies. Primary antibodies targeting the HA tag (monoclonal ab9110, Abcam), FLAG tag (monoclonal 637301, BioLegend) and GFP (polyclonal A-11122, Thermofisher) were all used at a concentration of 1/3000. Biotinylated proteins were detected directly using streptavidin-horse radish peroxidase conjugate (RPN1231, Cytiva). Total proteins were visualised after separation using SYPRO ruby protein stain (Thermofisher).
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3

Detecting Protein Prenylation in RSV-Infected Cells

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HEp-2 cells were cultured in the presence of farnesyl alcohol azide (FAA) (SC-294586, Santa Cruz Biotechnology) or geranylgeranyl alcohol azide (GGAA) (C10249, Thermo Fisher Scientific) at a final concentration of 25 µM diluted in 10 mM aqueous NH4OH. Cells were infected with RSV A2 (MOI 0.5) and treated with drugs 2 h post-viral exposure. Cell lysis was performed on ice in RIPA buffer 48 h p.i., and prenylated proteins were reacted with biotin-PEG4-alkyne using the Click-iT Protein Reaction Buffer Kit (C10276, Thermo Fisher Scientific) as per the manufacturer’s protocol. Prenylated proteins in the processed samples were then visualized by western blot using a streptavidin-HRP conjugate (RPN1231, Cytiva) and Clarity ECL Substrate (1705061, Bio-Rad). Relative protein levels were quantified by densitometry in ImageJ (v1.52b).
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4

Western Blot Antibody Detection

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Amersham ECL mouse IgG HRP-linked whole Ab; sheep polyclonal at 1:10 000 dilution (NA931V, Cytiva)
Streptavidin–horseradish peroxidase conjugate at 1:10 000 dilution (RPN1231, Cytiva)
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5

Western Blot Analysis of Protein Samples

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Total cell lysates were boiled for 10 min at 99°C in 1× Laemmli buffer supplemented with 4.2% (vol/vol) β-mercaptoethanol. Proteins were separated by electrophoresis on precast 4 to 20% SDS-PAGE gels (Bio-Rad Laboratories) and semidry blotted on nitrocellulose membranes. Membranes were blocked with a 5% (wt/vol) lowfat milk solution in PBS. Proteins were detected with the following primary antibodies: rabbit anti-Flag (F7425; Sigma-Aldrich), rabbit anti-HA (ab9110; Abcam), and rabbit anti-MED25 (NBP2-55868; Novus Biologicals). As a control for equal loading, we used mouse anti-α-tubulin (T5168; Merck) or rabbit anti-glyceraldehyde-3-phosphate dehydrogenase (anti-GAPDH) (ab9485; Abcam). We used the following secondary antibodies: streptavidin-horseradish peroxidase (HRP) (RPN1231; Amersham Life Science), ECL donkey anti-rabbit IgG–HRP (NA934V, GE Healthcare), and ECL sheep anti-mouse IgG–HRP (NA931V; GE Healthcare). Protein bands were visualized by using Pierce ECL Western blotting substrate (32106; Thermo Fisher Scientific) and a chemiluminescence imager (Amersham Imager 600; GE Healthcare).
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6

Neurobiotin-Injected Brain Tissue Processing

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The Neurobiotin-injected tissues were fixed overnight at 4°C with 4% PFA and 1% glutaraldehyde (GA) in 0.067 M phosphate buffer (PB, pH 7.4) containing 1% saturated picric acid. After fixation, the brain was dissected and embedded in a gelatin/albumin mixture (4.8% gelatin and 28% albumin in distilled water) and then post-fixed overnight at 4°C in 7–8% PFA in PB. The post-fixed tissues were sectioned in a frontal plane at a thickness of 40 μm with a vibrating blade microtome, then washed in PB, and incubated overnight at 4°C with streptavidin-horseradish peroxidase (HRP, 1:200; RPN1231, Amersham Biosciences, Bucks, UK) in 0.01 M phosphate-buffered saline (PBS, pH 7.4) containing 0.5% Triton X (PBST). The sections were developed with a solution of 0.032% 3,3’-diaminobenzidine tetrahydrochloride (DAB) in 0.1M Tris-HCl (pH 7.4) containing 0.0145% H2O2 and 0.3% nickel ammonium sulfate. After washing in PB, the sections were mounted on a gelatin-coated glass slide, dehydrated in a graded ethanol series, cleared in xylene, and mounted in Mount-Quick (Daido Sangyo, Tokyo, Japan) beneath a cover slip.
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