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8 protocols using rpa194

1

Protein Expression Analysis in Cell Lines

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TIAR (Santa Cruz, sc-1749), NPM (Santa Cruz, sc-70392), FBL (Cell signaling Technology, 2639), RPA194 (Santa Cruz, sc-4669), eIF2α (Santa Cruz, sc-133132), phospho-eIF2α (AbCam, 131505), 4EBP (Cell Signaling Technology, 9454), non-phospho-4EBP (Cell Signaling Technology, 4923S), TIF-IA/RRN3 (Santa Cruz, 2c-390464), RPL7A (Cell Signaling Technology, 2415) Nol9 (Protein Tech Group, 16083-1-AP), UBF (Santa Cruz, sc-13125), eIF3B (Santa Cruz, sc-16377)
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2

Immunocytochemistry of Nucleolar Proteins in mES Cells

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E14 mES cells were grown on gelatin-coated glass coverslips with MEFs and cultured 12 h before fixed with 4% PFA for 10 min, and then permeabilized with 0.5% Triton X-100 in PBS for 20 min at room temperature (RT). The cell samples were blocked in blocking buffer (3% BSA, 2% donkey serum in PBS) for 10 min at RT and then stained with a primary antibody (1:100, Nucleolin, CST, cat. no. 145745; 1:500, NPM1, Sigma, cat. no. B0556; 1:100, Fibrillarin, Abcam, cat. no. ab4566; RPA194, 1:200, Santa Cruz, cat. no. sc-48385) for 12 h at 4 °C. After three washes with 0.1% Triton X-100 in PBS, cells were stained with a secondary antibody (1:200, Goat polyclonal Secondary Antibody to Mouse IgG, Abcam, cat. no. ab150113) for 2–12 h at 4 °C. Followed by washing three times with 0.5% Triton X-100/PBS, DAPI was used for nucleus staining. The samples were then imaged by Zeiss LSM880 fluorescence microscope at a 63× oil objective. For high regulation microscopy imaging, LSM800 with Airyscan module was used.
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3

Immunofluorescence Staining of Nuclear Proteins

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Cells were seeded on coverslips in a 24-well plate, washed with PBS (Biological Industries, Israel), and fixed with 4% formaldehyde in PBS for 25 min at room temperature. After fixation, cells were washed with PBS, and permeabilized and blocked in PBS containing 0.2% Triton X-100% and 1% BSA. Slides were incubated with primary antibodies to UBF (Sigma/Santa Cruz, CA, USA), Fibrillarin (Abcam, Cambridge, UK), NPM (Abcam, Cambridge, UK), Nucleolin (Abcam, Cambridge, UK), RPA194 (Santa Cruz, CA, USA), PICT-1 (Santa Cruz, CA, USA), PML (Santa Cruz, CA, USA), ORF45 (Santa Cruz, CA, USA), ORF65 [64 (link)] (a kind gift from Shou Jiang Gao) or ORF59 (a kind gift from Prof. Bala Chandran, University of South Florida) [65 (link)] at 40 C, followed by incubation with secondary conjugated antibodies (Rhodamine, Cy3, Alexa Fluor 647 or Alexa Fluor 488, Jackson ImmunoResearch Laboratories, Inc., West Grove, PA) for 1 h at room temperature. To stain the nuclei, cells were incubated for 10-min with 0.05 µg/mL Hoechst dye (Sigma) in PBS. The slides were mounted with anti-fading medium (1% n-Propyl gallate, 90% Glycerol in PBS). Cells were examined and photographed under a confocal laser-scanning microscope (Leica SP8 Confocal Live Microscope).
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4

Immunofluorescence Staining of Nuclear Proteins

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Cells were fixed in 4% paraformaldehyde for 15 min and washed in phosphate-buffered saline (PBS) three times of 10-min each before permeabilized by 0.2% Triton-X 100/PBS for 10 min and additional PBS wash three times. Primary antibodies were then incubated for 1 h at room temperature. They are from the indicated sources and used at the stated dilutions: RPA194, Santa Cruz Biotechnology, catalogue#sc-48385, 1:100; PTB (S. Huang laboratory), 1:300; UBF, Santa Cruz Biotechnology, catalogue#: sc-13125, 1:50; fibrillarin, Sigma, catalogue#: ANA-N, 1:10; CENPA (Thermo Fisher #MA1-20832, 1:100; coilin, Santa Cruz Biotechnology, catalogue#: sc-32860, 1:300; Flash histone locus protein (Joseph Gall, Carnegie Institution for Science), 1:500; SMN, Santa Cruz Biotechnology, catalogue# sc-15320, 1:300, SC-35 1:200 (David Spector, Cold Spring Harbor Laboratory). After incubation with primary antibodies, the fluorescein-conjugated (Jackson ImmunoResearch) and Alexa Fluor-labeled (ThermoFisher Scientific ) secondary antibodies were incubated with cells at a dilution of 1:200 for 1 h at room temperature. Cell bearing coverslips were then mounted with Vector mounting media. Slides were visualized on a Nikon Eclipse Ti-E inverted fluorescence microscope using NIS-Elements AR 4.2 software (Nikon).
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5

Immunofluorescence Staining of Embryos

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Embryos were first fixed with 1 and 2% paraformaldehyde (PFA) in 1× PBS for 3 min sequentially, followed by treatment with 4% PFA for 30 min at room temperature (RT). Embryos were washed three times with 1× PBS, permeabilized for 15 min in PBS/0.25% Triton X-100 and blocked-in blocking buffer (PBS/0.2% BSA/0.01% Tween-20) for 1 h at RT, followed by incubation overnight with primary antibodies (1:200, Nucleolin, CST, 145745; 1:400, NPM1, Sigma, B0556; 1:200, Fibrillarin, Abcam, ab4566; RPA194, 1:50, Santa Cruz, sc-48385) at 4° or for 1 h at 37 °C. Subsequently, embryos were washed four times for 10 min each and incubated with a secondary antibody (daylight 488-conjugated anti-rabbit, 1:100 or daylight 594-conjugated anti-mouse, 1:200) for 1 h at 37 °C and washed three times with PBS. Nuclei were stained with DAPI for 1 min. Embryos were observed under Zeiss LSM880 fluorescence microscope at 63× magnification with an oil immersion objective.
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6

Immunofluorescence Staining and Microscopy

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Primary antibodies were from the indicated sources and used at the stated dilutions: RPA194, Santa Cruz Biotechnology, cat #sc-48385, 1:100; PTB (S. Huang laboratory), 1:300; UBF, Santa Cruz Biotechnology, cat#: sc-13125, 1:50; fibrillarin, Sigma, cat #: ANA-N, 1:10; CENPA (Thermo Fisher #MA1-20832, 1:100; coilin, Santa Cruz Biotechnology, cat#: sc-32860, 1:300; Flash histone locus antibody protein (Gall lab), 1:500; SMN, Santa Cruz Biotechnology, cat.# sc-15320, 1:300. The fluorescein conjugated (Jackson ImmunoResearch) and Alexa Fluor-labeled (ThermoFisher) secondary antibodies were used at a dilution of 1:200. Slides were visualized on a Nikon Eclipse Ti-E inverted fluorescence microscope using NIS-Elements AR 4.2 software (Nikon).
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7

Polyclonal Antibody Production for HERC2

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Rabbit polyclonal antibody against the C-terminal region of HERC2, generated against recombinant HERC2 protein (residues 4389–4834), was established as per previously described methods27 (link). The commercially available antibodies used in the study were: rabbit polyclonal antibodies against BLM (Bethyl Laboratories, A300-110A), WRN (Bethyl Laboratories, A300-239A), BRCA1 (Santa Cruz Biotechnology, C20), mouse monoclonal antibodies against HERC2 (epitope 1781–1974, BD Biosciences, 17), NPM1 (Zymed Laboratories Inc), FBL (Abcam, 38F3), RPA194 (Santa Cruz Biotechnology, C1), RPA2 (Calbiochem, RPA34-20 NA19L), and α-tubulin (Neomarkers, DM1A, MS-581-P).
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8

Comprehensive Immunofluorescence Staining Protocol

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Following primary antibodies were used in this study: lamin B (Santa Cruz cat. no. sc-6217); filamin (Santa Cruz cat. no. sc-28284); alpha-actinin-4 (Abcam cat. no. ab96866); spectrin (Sigma Aldrich cat. no. S1390); paxillin (Millipore cat. no. 05-471); vinculin (Sigma Aldrich cat. no. V4505); mDia1 (BD Biosciences cat. no. P66520-050); SUN2 (Abcam cat. no. ab124916); emerin (Abcam cat. no. ab40688); Arp3 (Welch et al. 1997 (link)); cofilin (Abcam cat. no. ab11062); P-cofilin (Cell Signaling cat. no. 3313); Arp6 (Sigma Aldrich cat. no. R35554); Arp5 (Kitayama et al. 2009 (link)); Arp8 (Aoyama et al. 2008 (link)); Brg1 (Abcam cat. no. ab70558); hnRNP U (Santa Cruz, clone 3G6); H3K9Me2 (Millipore cat. no. 17-648); H3K4Me2 (Millipore cat. no. 07-030); CTD-phosphoS2 (Abcam cat. no. ab24758); RPA194 (Santa Cruz, cat. no. sc-28714); and BrdU (Sigma Aldrich, clone BU-33).
Secondary antibodies used in this study are donkey anti-rabbit IgG conjugated with Alexa Fluor 568 (A10042), goat anti-mouse IgG conjugated with Alexa Fluor 647 (A21236) and donkey anti-goat IgG cojugated with Alexa Fluor 647 (A21447) all purchased from Life Sciences.
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