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8 protocols using mab flag m2

1

Western Blot Analysis of HCMV Proteins

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Immediately following cell culture supernatant harvest, cells were washed with phosphate buffered saline (PBS) and harvested using 0.25% trypsin. Cells were washed with PBS and lysed with 2X SDS sample buffer (62.5 mM Tris/HCl (pH 6.8), 1 mM EDTA, 10% glycerol, 2% SDS, 5% β-mercaptoethanol, 0.005% bromophenol blue) at 95°C for 10 min followed by a brief vortex. Protein extracts were subjected to SDS-PAGE followed by transfer to a Protran nitrocellulose membrane (Whatman). Immunostaining was performed with the antibodies mAb-β-actin (Ac-15, Sigma), mAb-Flag (M2, Sigma), mAb-IE1p72/pUL44 (Clones DDG9 and CCH2; Dako), mAb-IE2p86 (Santa Cruz), mAb-pp65 (Abcam), mAb-pUL97 (#8, kindly provided by Detlef Michel, Ulm, Germany), mAb-MCP (major capsid protein; 28-4, kindly provided by William Britt, Birmingham, AL, USA) and HRP-conjugated anti-mouse secondary antibody (Pierce). Protein bands were visualised using chemiluminescence. Densitometry of immunostaining was performed using ImageJ software. The mean densitometry values for control infected-cells were assumed to be 100% and this value was used to calculate relative protein expression in HCMV-infected cells treated with HCMV siRNAs with results presented as mean ± SD of duplicate or triplicate biological experiments.
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2

Western Blot of Transfected Cell Lysates

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Lysates from transfected cells were boiled with 4× SDS buffer for 10 min at 95 °C. The lysates were then sonicated for 1 min using the QSonica Q700 Sonicator (QSonica, Newton, MA, USA). Next, the samples were separated on 10% SDS polyacrylamide gels and transferred to PVDF membranes (BioRad, Feldkirchen, Grmany), followed by chemiluminescence detection using a FUSION FX7 imaging system (Vilber Lourmat, Eberhardzell, Germany). Following antibodies were used: mAB Flag M2 (Sigma-Aldrich, St. Louis, MO, USA), pAB human STAT2 H190 (Santa Cruz, Dallas, TX, USA), mAB β-Actin AC15 (Sigma-Aldrich, St. Louis, MO, USA), mAB Halo (G921A, Promega, Fitchburg, MA, USA), pAB IE2 (pAB178; [28 (link)]).
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3

Culturing RK-13 and HEK293T cells

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RK-13 and HEK293T cells were cultured essentially as described previously (59 (link), 62 (link)). mAb 58-46 (α-EU-nsp2) (14 (link)), which recognizes the N-terminal domain of nsp2, nsp2TF, and nsp2N, was a kind gift from Dr. Ying Fang. mAb-FLAG (M2) was from Sigma.
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4

Western Blot Analysis of Cellular Proteins

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Lysates from transfected or infected cells were prepared in a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) loading buffer by boiling for 10 min at 95°C and sonication for 1 min. Proteins were separated on sodium dodecyl sulfate-containing 8 to 15% polyacrylamide gels and transferred to PVDF membranes (Biorad), followed by chemiluminescence detection using a FUSION FX7 imaging system (Vilber). Following antibodies were used: mAb FLAG M2 (Sigma-Aldrich), mAb Myc 9E10 (1-9E10.2; ATCC), mAb β-actin AC-15 (Sigma-Aldrich), mAb HCMV IE1 p63-27 [74 (link)], mAb RCMV IE1 (kindly provided by Sebastian Voigt), mAb PML 5E10 (kindly provided by Roel van Driel) was used to detect ratPML, and pAb PML A301-167A and A301-168A (Bethyl Laboratories) were used in combination to detect human PML.
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5

Immunoprecipitation Assay using Dynabeads

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The clarified lysate is incubated for 60 min with 25 μl Dynabeads™ Protein G beads (10003D, Thermo Fisher Scientific), coupled to 1 μl of FLAG-M2 mAb (Sigma, F1804) then washed once with NLB. The beads are then resuspended with 1 ml of NDB and the protocols described for XF1-4 above are followed exactly, in that XF5 ∼ XF1, XF6 ∼ XF2, XF7 ∼XF3 and XF8 ∼ XF4. For an overview of these protocols see Figure 2, Supplementary Figures S1 and S2.
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6

Immunodetection of FLAG-tagged Proteins

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U2AF65 (monoclonal mouse antibody Sigma U4758), Flag-HRP (Sigma A8592), FLAG-M2 mAb (Sigma, F1804).
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7

Generation of Custom Antibodies

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Custom Cep120, Ta3, Odf2, Cep164 antibodies were generated by Covance, Inc. Rabbits were immunized with insoluble His-tagged mouse Cep120 (660-E aa), Ta3 (1–430 aa), Odf2 (full-length), Cep164 (1–298 aa) protein fragments purified from bacteria. All these antibodies were used at a 1∶1000 dilution for both immunoblotting and immunostaining. Other antibodies used for immunofluorescence and Western blotting included Flag M2 mAb (1∶1000), acetylated tubulin (1∶2000), γ-tubulin (1∶2000) (Sigma), Arl13b (1∶1500) [24] (link), Calb1 (1∶200, cat #13176, Cell signaling), Pax6 (1∶50), and BrdU (1∶200) (DSHB, University of Iowa). Secondary antibodies Dylight 488-conjugated donkey anti rabbit IgG and Cy3-conjugated donkey anti mouse IgG were purchased from Jackson Immunoresearch, Inc.
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8

Rad53 Phosphorylation Measurement in DNA Damage

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Rad53 phosphorylation was assessed as described previously [9 (link)]. Briefly, exponentially growing cells (2-4x107 cells/ml) in mec1Δ sml1Δ or mec1Δ sml1Δ sae2Δ background were cultured in presence of 0.15% MMS for 90 min. MMS was inactivated upon addition of 5% sodium thiosulfate (final concentration) to the cultures. TCA-extracts were prepared and 10–20 μg protein extracts were run on a 7.5% SDS-PAGE, transferred to nitrocellulose membrane and FLAG-Rad53 was detected by western blot with FLAG M2 mAb (Sigma).
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