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7 protocols using anti ha

1

Immunoblot and Immunostaining Antibodies

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Antibodies used for the immunoblot and immunostaining were anti-p300 (BD Biosciences, San Jose, CA, USA), anti-α-tubulin (Sigma), anti-myc, anti-Flag, anti-GFP, anti-HA (abm, Richmond, Canada), anti-ubiquitin (Millipore, Billerica, MA, USA), anti-acetylated lysine (Cell signaling, Danvers, MA, USA). Anti-HIPK2 antibody was a kind gift of Dr. K. Isono (RIKEN, Japan) and described previously27 (link).
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2

Co-Immunoprecipitation of HA-tagged Rrp6p

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Samples were grown and harvested as previously stated. Cell lysates were prepared as indicated above, but with the Co-IP lysis buffer (50mM Tris-HCl pH 7.4, 50mM NaCl and 1% NP-40) supplemented with protease and phosphatase inhibitors (Roche). Approximately 1.5mg of protein lysates were incubated with 25uL of magnetic anti-HA beads (Pierce) for 1 h at 4°C. Samples were washed 6 times with lysis buffer and eluted in 40uL of 1 mg/mL HA Peptide (Sigma-Aldrich). 10uL of eluate and 5ug of total lysates were loaded onto each lane of a Nu-Page gel. Rrp6p was detected with anti-Rrp6 (1:5000, (Schuch et al., 2014 )) and HA tagged proteins were detected with anti-HA (1:5000, ABM). Secondary antibodies used were obtained from LI-COR (1:10000).
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3

Immunoprecipitation and Immunoblotting Assay

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Cells were harvested in lysis buffer (20 Mm Tris-HCl pH 8, 137 mM NaCl, 2 mM EDTA and 1% NP-40) with protease inhibitor cocktail at 4°C. Equal amounts of protein lysates were incubated with control IgG, anti-HA (ABM, G036), anti-Flag (Sigma, F1804), or anti-ephrinB1 (R&D systems, AF473) at 4°C overnight under mild agitation. Protein A/G-agarose beads (Santa Cruz Biotechnology) were then incubated for 1hr, followed by washing three times with lysis buffer. Immunoprecipitates and total protein lysates were separated by SDS-PAGE and immunoblotted with anti-HA-HRP (Roche, 12013819001), anti-Flag-HRP (Sigma, A8592), anti-V5 (Invitrogen, R961-25), anti-ephrinB1 (R&D Systems, af473) or anti-ephrinB (Santa Cruz Biotechnology C18, SC-910), anti-EphB2 (R&D Systems, AF467), anti-RhoGDI1 (Santa Cruz Biotechnology, SC-360) and anti-RhoA (Santa Cruz Biotechnology, SC-418), anti-Rac1 (Millipore, 05-389), anti-Cdc42 (BD Bioscience, 610929) and α-tubulin (Sigma, T6199).
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4

Antibody Selection for Protein Detection

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The following antibodies were used: anti-FLAG, anti-FLAG-HRP, anti-HA, anti-HA-HRP (Sigma Aldrich), anti-FLAG, anti-HA, anti-GST (abm), anti-GST, anti-His (Santa cruz biotechnology), anti-H1, H2A, H2B (Abcam) and anti-H3, H4, H3K9Ac, H3K27Ac, H3K4me3, H3K9me2, H3K27me2 (Upstate).
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5

Protein Immunoprecipitation and Immunoblotting

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Cells were harvested in ice-cold RIPA buffer (100 mM Tris–HCl pH 7.6, 50 mM NaCl, 50 mM β-glycerophosphate, 50 mM NaF, 0.1 mM Na3VO4, 0.5% NP-40, 0.5% sodium deoxycholate and 5 mM EDTA) with protease inhibitor cocktail. Quantified protein lysates were incubated with anti-Flag (Sigma, F1804) and anti-HA (ABM, G036) at 4 °C overnight, followed by agarose beads were incubated for 2 h. Total protein lysates and immunoprecipitates were subjected to immunoblotting with anti-Flag-HRP (Sigma, A8592), anti-HA-HRP (Roche, 12013819001), anti-PLK1 (Cell Signaling Technology, 4513), anti-PLK1 (Santa Cruz Biotechnology, sc-17783), anti-RhoGDI1 (Santa Cruz Biotechnology, sc-373724), anti-RhoGDI1 (invitrogen, 51-1000Z), anti-GST (Santa Cruz Biotechnology, sc-138), anti-His (Santa Cruz Biotechnology, sc-8036), anti-Phospho-(Ser/Thr) (Cell Signaling Technology, 9631), anti-RhoA (Santa Cruz Biotechnology, sc-418), anti-Rac1 (Millipore, 05-389), anti-Cdc42 (BD Bioscience, 610929) and β-Actin (Santa Cruz Biotechnology, sc-47778).
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6

Co-Immunoprecipitation of HA-tagged Rrp6p

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Samples were grown and harvested as previously stated. Cell lysates were prepared as indicated above, but with the Co-IP lysis buffer (50mM Tris-HCl pH 7.4, 50mM NaCl and 1% NP-40) supplemented with protease and phosphatase inhibitors (Roche). Approximately 1.5mg of protein lysates were incubated with 25uL of magnetic anti-HA beads (Pierce) for 1 h at 4°C. Samples were washed 6 times with lysis buffer and eluted in 40uL of 1 mg/mL HA Peptide (Sigma-Aldrich). 10uL of eluate and 5ug of total lysates were loaded onto each lane of a Nu-Page gel. Rrp6p was detected with anti-Rrp6 (1:5000, (Schuch et al., 2014 )) and HA tagged proteins were detected with anti-HA (1:5000, ABM). Secondary antibodies used were obtained from LI-COR (1:10000).
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7

Immunoprecipitation and Immunoblotting Assay

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Cells were harvested in lysis buffer (20 mm Tris-HCl pH 8, 137 mm NaCl, 2 mm EDTA and 1% NP-40) with protease inhibitor cocktail at 4 °C. Equal amounts of protein lysates were incubated with control IgG, anti-HA (ABM, Richmond, BC, Canada, G036), anti-Flag (Sigma, Allentown, PA, USA, F1804), or anti-ephrinB1 (R&D systems, AF473) at 4 °C overnight under mild agitation. Protein A/G-agarose beads (Santa Cruz Biotechnology, Santa Cruz, CA, USA) were then incubated for 1 h, followed by washing three times with lysis buffer. Immunoprecipitates and total protein lysates were separated by SDS–PAGE and immunoblotted with anti-HA-HRP (Roche, Billerica, MA, USA, 12013819001), anti-Flag-HRP (Sigma, A8592), anti-V5 (Invitrogen, Carlsbad, CA, USA, R961-25), anti-ephrinB1 (R&D Systems, af473) or anti-ephrinB (Santa Cruz Biotechnology C18, SC-910), anti-EphB2 (R&D Systems, AF467), anti-RhoGDI1 (Santa Cruz Biotechnology, SC-360) and anti-RhoA (Santa Cruz Biotechnology, SC-418), anti-Rac1 (Millipore, Billerica, MA, USA, 05-389), anti-Cdc42 (BD Bioscience, San Jose, CA, USA, 610929) and α-tubulin (Sigma, T6199).
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