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4 protocols using h3663

1

HEK293T Cell Immunoprecipitation and Western Blot

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HEK293T cells transfected with different combinations of plasmids were harvested and resuspended in 1 ml ice-cold Pierce IP buffer (87787) containing protease inhibitors (Complete Mini EDTA-free, Roche and PMSF) and phosphatase inhibitor (NaF and NaVO3). Cells were lysed for 30 min at 4 °C and lysates were spun for 30 min at maximum speed at 4 °C. 20–40 μl anti-Flag M2 beads (Sigma, M8823) were added to the cell lysate and incubated overnight. Beads were washed five times with immunoprecipitation buffer and, finally, bound proteins eluted by boiling in loading buffer. Samples were separated on 4–12% Tris-Bis gels (Life Technology) and transferred onto PVDF membranes (Whatman). Western blot analysis was performed using antibodies against Flag (Sigma, F1804 or F7425), HA (Sigma, H3663 or Abcam, ab9110), Casp1 p10 (Santa Cruz, sc-514), DHX9 (Abcam, ab26271), DHX15 (Abcam, ab70454 or ab13311), Casp3 p17/p19 (Cell Signaling, 9661), LC3 (Cell Signaling, 2775), or β-actin (Sigma, A1978).
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2

PPM1H Regulation of Phospho-Rab10

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MEF cells stably expressing GFP-Rab10 were transiently transfected with plasmids carrying wild-type HA-PPM1H, HA-PPM1H[H153D], or HA-PPM1H[D288A]. After 24 h the cells were fixed with 4% (by vol) paraformaldehyde for 10 min, permeabilized with 0.1% saponin for 15 min, and blocked with 1% (by mass) BSA for 1 h. Cells were subsequently stained with mouse anti-HA antibody 1:1000 (Sigma-Aldrich H3663) and rabbit phospho-Rab10 1:1000 (Abcam ab230261). Highly cross absorbed H+L secondary antibodies (Life Technologies) conjugated to Alexa 568 or Alexa 647 were used at 1:5000. Primary and secondary antibody incubations were for 1 h at room temperature. All images were obtained using a spinning disk confocal microscope (Yokogawa) with an electron multiplying charge coupled device (EMCCD) camera (Andor, UK) and a 20x1.4NA or 40x1.4NA objective. Images were analyzed using CellProfiler and presented as maximum intensity projections. Results were quantified by determining the ratios of phospho-Rab10 signal to GFP-Rab10 in cells expressing wild-type HA-PPM1H, HA-PPM1H[H153D], or HA-PPM1H[D288A], and normalizing these numbers to the phospho-Rab10/GFP-Rab10 ratio in non-expressing cells. For each condition at least 20 cells were analyzed. Significance was determined by one-way analysis of variance with Dunnett's post-test at 95% confidence interval. ***, P < 0.001.
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3

Immunocytochemical Analysis of Cellular Proteins

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For immunocytochemical analysis, cells were fixed in a 4% paraformaldehyde solution in PBS for 10 min at room temperature (RT), permeabilized in a 0.5% Triton-X-100 solution in PBS for 5 min and blocked for 1 h with 3% BSA in PBS. Immunostaining was performed by addition of the primary antibodies (mouse anti-HA, Sigma Aldrich, H3663, 1:1000; rabbit anti-GRP75, Abcam, ab53098; 1:5000; goat anti-c-myc, Novus Biologicals, NB600335, 1:500) in the blocking solution overnight at 4 °C and the appropriate fluorescently labelled secondary antibodies for 1 h at RT. Nuclei were stained by addition of DAPI. Images were acquired using a Leica SP8-X confocal microscope (Leica Microsystems) and analyzed using Imaris software (Oxford Instruments).
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4

PCNA Library Screening Protocol

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Assay specific strains were constructed with genotype listed in table S5. The reporter strain used for PCNA library construction and screening is QJY001. Antibodies used were anti-HA (Sigma-Aldrich, H3663), anti-PCNA (Abcam, 5E6/2), and H3 (Abcam, ab1791), anti-SMT3 (Abnova, MAB2093).
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