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8 protocols using anti pcna pc10

1

Mitochondrial Enzyme Profiling in Ercc1 Mice

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Liver and kidney samples from 18-week-old Ercc1/Δ and WT mice (n = 5) were homogenized in RIPA buffer (Pierce, Rockford, IL) with protease inhibitor cocktail (Roche, Indianapolis, IN). Mitochondrial extracts were prepared using Mitochondria Isolation Kit (Pierce) per the manufacturer’s specifications. Samples were separated on 4–20% polyacrylamide gel (Bio-Rad, Hercules, CA), transferred to nitrocellulose membrane, blocked and blotted with anti-PCNA (PC10, Santa Cruz Biotechnology, Santa Cruz, CA), anti-ERCC1 (D-10, Santa Cruz Biotechnology), anti-COXIV (Abcam, Cambridge, MA), anti-XPF (SPM228, Novus Biologicals, Littleton, CO) or anti-GAPDH, anti-MnSOD, anti-CuZnSOD, anti-catalase (3H3L29), anti-XO, and anti-rabbit secondary (all from Life Technologies, Carlsbad, CA) then visualized with ECL reagent (Pierce). Films exposed to membrane were imaged with ImageJ (NIH, Bethesda, MD). GAPDH was used as a loading control.
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2

TRAIP Antibody Production and Validation

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The TRAIP polyclonal antibody was raised against GST-TRAIP-N terminal fusion protein (see Figure 3e) and affinity purified using column coated with MBP-TRAIP-N terminal fusion protein. Antibody specifically recognizing γH2AX was previously described [42 (link)]. The anti-PCNA (PC10) and anti-CHK1 (G-4) antibodies were from Santa Cruz (Dallas, TX, USA); anti-Ki67 antibodies were from Chemicon (Darmstadt, Germany); anti-RPA1 antibodies were from Calbiochem (Darmstadt, Germany); anti-Chk1-pS345 antibodies were from Cell Signaling (Danvers, MA, USA); anti-KAP1 antibodies were from BD Transduction Laboratories (San Jose, CA, USA). Anti-Actin, anti-GFP and anti-Flag (M2) antibodies were obtained from Sigma (Darmstadt, Germany). ATMi (KU55993) and ATRi (VE821) inhibitors were from SelleckChem (Houston, TX, USA).
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3

Cryosectioning and Immunostaining of Fixed Embryos

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Embryos were fixed in either 4% PFA, Dent fixative or 1% TCA for 1-3 days and subjected to cryosectioning as described previously31 (link). Antibodies used were: anti-FN antibody (Ab), Sigma F3648 at 1:100; β-integrin monoclonal Ab, 8c8 (Developmental Studies Hybridoma Bank, USA) at 1:10; anti-aPKC C-20 (SC216, Santa Cruz Biotech, USA) at 1:100; anti-PCNA (PC10, Santa Cruz Biotech, USA) at 1:500; anti-laminin (Ab-1, NeoMarkers, USA) at 1:100 and anti-ZO-136 (link) (gift from Dr M Itoh) at 1:1. Sections were counterstained with Alexa Fluor 488 or 546 Phalloidin (A12379, A22283, Invitrogen USA) at 1:250 and TO-PRO-3 (T3605, Invitrogen, USA) at 1:1000.
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4

DNA Damage Response Pathway Assay

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The following antibodies were obtained from commercial sources: anti-DNA:RNA (S9.6, Kerafast); anti-DDDDK-tag (MBL); anti-FLAG (M2, Sigma-Aldrich); anti-FLAG M2 magnetic beads (Sigma); normal mouse IgG (Santa Cruz); anti-FANCA (Bethyl); anti-FANCD2 (Novus); anti-PCNA (PC10, Santa Cruz); anti-γH2AX (JBW301, Millipore); anti-RPA (9H8, Abcam); anti-a-tubulin (T5168, Sigma). Aphidicolin (Wako), mitomycin C (MMC) (Kyowa Hakko Kirin), or cordycepin (Wako) were used at the indicated concentrations. Primers and siRNA oligos are summarized in Supplemental Table S1.
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5

Antibody-based Western Blot Analysis Protocol

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Antibodies used for Western blot analysis included the following: anti-C1orf55/SDE2 (epitope: a.a. 318–410; Sigma-Aldrich), anti-GFP (JL-8, Clontech), anti-HA (6E2, Cell Signaling), anti-pCHK1 (S317, Cell Signaling), anti-Actin (Cell Signaling), anti-CDT1 (Cell Signaling), anti-Flag (M2, Sigma-Aldrich), anti-Tubulin (Sigma-Aldrich), Cyclin E (H-12, Santa Cruz), anti-PCNA (PC-10, Santa Cruz), anti-Vinculin (H-300, Santa Cruz), anti-GST (B-14, Santa Cruz), Cyclin A (H-432, Santa Cruz), anti-γH2AX (JBW301, Millipore), anti-CDT2 (Bethyl), anti-pRPA (S33, Bethyl), pKAP-1 (S824, Bethyl), anti-ORC2 (BD Pharmingen), and anti-MUS81 (MTA30 2G10/3, Abcam). Mitomycin C, camptothecin, hydroxyurea, cycloheximide, aphidicolin, and Z-Leu-Leu-Leu-al (MG132) were purchased from Sigma-Aldrich. Rucaparib (AG-014699) was purchased from Selleckchem. MLN4924, ubiquitin vinyl sulfone, and ubiquitin aldehyde were purchased from Boston Biochem. Drugs were used at the concentrations indicated in the figure legends.
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6

Quantitative Analysis of PCNA in Bladder Cancer

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Bladder cancer cells were grown on glass bottom dishes and stained with anti-PCNA (PC10; Santa Cruz Biotechnology Inc) and Alexa Fluor 532 goat anti-mouse (Invitrogen, Carlsbad, CA, USA) antibodies and DRAQ5 (eBioscience, San Diego, CA) as described [15] (link). The relative intensities of PCNA in cytosol/nuclei were calculated using mean region of interest containing at least 400 pixels using the Zeiss LSM 510 software.
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7

Protein Expression Analysis in Cell Lysates

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Samples were collected and placed on ice in a lysis solution [50 mM Tris–HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA, 1% NP-40, 10% glycerol] containing 0.5% SDS and 2 mM PMSF with a protease inhibitor cocktail (Sigma P-8340, 1:100). Cellular proteins were resolved on a 12.5% SDS–PAGE gel. The membrane was incubated for 1 h at room temperature in 5% skim milk in PBS with 0.05% Tween-20 (PBST), and the membrane was probed with anti-PCNA PC10 (Ref # sc56; Santa Cruz), anti-alpha tubulin (Ref# MA1-80017; Thermo Fisher Scientific), anti-actin (Ref #MA1-744; Thermo Fisher Scientific), anti-Vinculin (clone 7F9, Ref# 14-9777-80; eBioscience), anti-AID (Ref #14-959-82; Thermo Fisher Scientific), anti-polη (Ref# ab17725; Abcam), anti-FancD2 (Ref# sc20022; Santa Cruz), anti-USP1 (Ref # ab108104Ref; Abcam), anti-Msh2 (Ref #A300-451A; Bethyl), and anti-Msh6 (Ref # A300-022A; Bethyl) antibodies. Immunoreactivity was detected using a horseradish peroxidase-conjugated secondary antibody.
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8

Cryosectioning and Immunostaining of Fixed Embryos

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Embryos were fixed in either 4% PFA, Dent fixative or 1% TCA for 1-3 days and subjected to cryosectioning as described previously31 (link). Antibodies used were: anti-FN antibody (Ab), Sigma F3648 at 1:100; β-integrin monoclonal Ab, 8c8 (Developmental Studies Hybridoma Bank, USA) at 1:10; anti-aPKC C-20 (SC216, Santa Cruz Biotech, USA) at 1:100; anti-PCNA (PC10, Santa Cruz Biotech, USA) at 1:500; anti-laminin (Ab-1, NeoMarkers, USA) at 1:100 and anti-ZO-136 (link) (gift from Dr M Itoh) at 1:1. Sections were counterstained with Alexa Fluor 488 or 546 Phalloidin (A12379, A22283, Invitrogen USA) at 1:250 and TO-PRO-3 (T3605, Invitrogen, USA) at 1:1000.
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