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7 protocols using ab10297

1

Co-immunoprecipitation of Protein Complexes

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Co-immunoprecipitation (Co-IP) was performed as previously described [9 (link), 12 (link), 14 (link)], with antibodies specific for hnRNPU (ab10297), CTCF (ab188408), FLAG (ab125243), or Myc (ab9106, Abcam Inc.). Bead-bound proteins were released and analyzed by Western blot.
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2

Mapping Spliceosomal Protein-RNA Interactions

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The full length M1 mRNA was transcribed from a linearized plasmid-based template by T7 polymerase using 32P-CTP to 32P- label the RNA throughout its length. Labeled M1 mRNA (10 nM) was incubated with 40% JSL1 nuclear extract in a total volume of 10.2 µl under splicing condition, which contains (final concentration): 12 mM Tris-HCl, pH 7.5, 3.2 mM MgCl2, 1 mM ATP, 20 mM CP, 0.12 mM EDTA, 60 mM KCl, 1.3% PVA, 250 ng yeast tRNA, 200 ng BSA, and 12% glycerol. Reactions were incubated at 30°C for 20 min, crosslinked using UV light (254 nm) for 20 min on ice, and digested with RNaseT1 and RNase A for 20 min at 37°C. Reactions were resuspended in 2× SDS loading buffer, denatured for 5 min at 95°C, analyzed under denaturing conditions on an SDS-PAGE gel (Acrylamide/Bis 37.5:1, BioRad), and detected by autoradiography. Immunoprecipitation after crosslinking was carried out with the antibodies against SON (GTX129778 GeneTex), UAP56 (SAB1307254 Sigma), AlyRef (A9979 Sigma), and hnRNP U (ab10297 abcam).
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3

Protein Extraction and Western Blot Analysis

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Cell samples were washed with precooled 0.1 M PBS and then lysed with cell lysis solution (RIPA). Ice bathing was conducted for 30 min, followed by centrifugation at 12000 rpm at 4°C for 10 min. The supernatant was collected and preserved at –20°C for further use. BSA (2 μg/μl) was diluted with 0.1 M PBS to the following concentrations: 20, 15, 10, 5, 2.5, and 0 μg/ml. Protein concentration was detected using BCA (Thermo Fisher Scientific Inc., MA, U.S.A.) according to the instructions and sample numbers. The protein was electrophoresed in a 4°C chromatography cabinet with 80 V of compressive gel and 120 V of separation gel. The electrophoresed proteins were transferred on to a PVDF membrane, blocked in TBST (25 mM Tris, 140 mM NaCl, and 0.1% Tween 20, pH 7.5) containing 5% skimmed milk and incubated for 2 h. The proteins were combined with the primary antibody of p120 (1:500; article number ab10297; ABCAm Inc., Cambridge, MA, U.S.A.) and β-actin (1:10000; article number ab8226; ABCAm Inc., Cambridge, MA, U.S.A.) and incubated at 4°C overnight. After being washed (3 × 10 min) with TBST, the secondary antibody was added and incubated at room temperature for 1 h. Subsequently, the cells were rewashed with TBST (3 × 10 min) and chemiluminescence was conducted. The results were analyzed according to the developed and fixed X-ray films.
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4

Western Blot Analysis of Cellular Proteins

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Tissue or cellular protein was extracted with 1 × cell lysis buffer (Promega, Madison, WI). Western blot was performed as previously described [9 (link), 11 (link)–15 (link)], with antibodies for HNF4A (ab181604), hexokinase 2 (HK2, ab104836), solute carrier family 2 member 1 (SLC2A1, ab40084), v-myc avian myelocytomatosis viral oncogene neuroblastoma-derived homolog (MYCN, ab16898), hnRNPU (ab10297), CTCF (ab188408), clusterin (CLU, ab69644), C-X-C motif chemokine receptor 4 (CXCR4, ab124824), trophoblast glycoprotein (TPBG, ab129058), uveal autoantigen with coiled-coil domains and ankyrin repeats (UACA, ab99323), FLAG (ab125243), Myc (ab9106), glutathione S-transferase (GST, ab19256), histone H3 (ab5103), or β-actin (ab6276, Abcam Inc., Cambridge, MA).
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5

Immunofluorescence Staining of Chromatin-Associated Factors

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Cells were washed in PBS and either (1) fixed in 4% PFA to reveal total protein or (2) treated with detergent prior to fixing to reveal chromatin- and NM-associated factors prior to incubation with primary antibody for 2 h, and then secondary antibody for 1 h. For the ESC differentiation course, PGK12.1 cells were fixed in 2% formaldehyde for 15 min prior to permeabilization. The antibodies used were α-H3K27me3 mAb (Abcam, ab6002; Active Motif, ab61017), α-CIZ1 N-terminal (1794), α-CIZ1 C-terminal (Novus, NB100-74624), SAFA anti-HNRNP-U (Abcam, ab10297), and anti-YY1 (SC7341). Coverslips were costained with limiting concentrations of Hoechst 33258 (10 ng/mL; Sigma) for quantitative detection of chromatin.
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6

Immunocytochemical Localization of hnRNPU

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Cells were plated on coverslip, incubated with 5% milk for 1 h, and treated with antibody specific for hnRNPU (ab10297, Abcam Inc., 1:300 dilution) at 4 °C overnight. Then, coverslips were treated with Alexa Fluor 594 goat anti-rabbit IgG (1:1000 dilution) and stained with DAPI (300 nmol·L−1). The images were photographed under a Nikon A1Si Laser Scanning Confocal Microscope (Nikon Instruments Inc, Japan).
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7

Immunofluorescence Microscopy Protocol

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Immunofluorescence was conducted with the same antibodies used for Western blots except for HNRNPU (Abcam, ab10297). The slides were imaged with a confocal laser scanning microscopy (Leica, SP5).
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