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6 protocols using rnase a

1

Isolation and Southern Blot Analysis of Genomic DNA

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Genomic DNA was isolated by spooling, following overnight incubation in Tail Buffer (1% SDS, 0.1 M NaCl, 0.1 M EDTA, 0.05 M Tris, pH8), treated with 50 μg/ml of RNase A (Amersham Biosciences) and cleaned using Qiagen Genomic-tip 100/G columns, following the manufacturer’s instructions. The Southern blot was prepared and probed as previously described (Rintala-Maki and Sutherland, 2009 (link)). The RBM5 probe was prepared using the PROSTAR HF single tube RT-PCR System (Stratagene), labelling with radioactive phosphate, and cleaning with a G25 sepharose column, following manufacturer’s instructions.
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2

Apoptosis Analysis of IFN-γ and TNF-α Treated Cells

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SK-N-MC cells (0.5 × 106 cells/6-well plate) were treated with IFN-γ (10 ng/mL) and TNF-α (20 ng/mL) alone or in combination for 48 h and assessed for apoptosis. Control and treated cells were harvested, washed in cold Phosphate buffered saline (PBS), and fixed in 70% ethanol and washed in PBS. The cells were centrifuged and the pellet was incubated with RNase-A (5 mg/mL) (Amersham Biosciences, Piscataway, NJ, USA) for 15 min followed by propidium iodide (50 µg/mL) for 2 h at 37 °C. DNA content was determined on the FL-2A channel with a flow cytometer (FACS Vantage, Becton Dickinson, San Jose, CA, USA) equipped with a 488 nm argon laser. Ten thousand events were scored for each sample and data was analyzed using CellQuest Pro software (BD Pharmingen, San Jose, CA, USA) for the analysis.
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3

Purification of HeLa Nuclear Proteins by Size Exclusion Chromatography

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HeLa nuclear extracts were obtained and dialyzed against buffer D containing 20 mM HEPES (pH 8.0), 10% glycerol, 0.1 mM EDTA, and 300 mM NaCl (Applygen Technologies, Beijing, China). ~6 mg of nuclear protein was concentrated to a final volume of 0.5 mL in a Millipore Ultrafree centrifugal filter apparatus (10 kDa nominal molecular mass limit), and then applied to an 850 × 20 mm Superose 6 size exclusion column (Amersham Biosciences) that was equilibrated with buffer D containing 1 mM dithiothreitol and calibrated with protein standards (blue dextran, 2000 kDa; thyroglobulin, 669 kDa; ferritin, 440 kDa; catalase, 232 kDa; bovine serum albumin, 67 kDa; and RNase A, 13.7 kDa) (Amersham Biosciences, Little Chalfont, UK). Nuclear protein was eluted using a flow rate of 0.5 mL/min, and fractions were collected.
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4

Molecular Techniques for Cell Analysis

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Trypsin-EDTA (1X), Dulbecco’s Modified Eagle Medium (DMEM), RPMI Medium 1640, and PSN Antibiotic mixture were purchased from Invitrogen (CA, USA). Fetal Bovine Serum (FBS) was purchased from Biosera (UK). Xylene cyanole and ethidium bromide (EB), Dimethylsulfoxide (DMSO) and other chemicals & reagents were purchased from Sigma Chemicals (St. Louis, USA). Sinigrin with 98% purity was purchased from Sigma-Aldrich (USA). RNase A was purchased from Amersham (USA).
ALT/SGPT (UV-Rate) & AST/SGOT (UV-Rate) Kits for detection of alanine and aspartate transferases were purchased from Stanbio Laboratory (TX, USA). Anti-GST-P polyclonal antibody (rabbit) was purchased from Medical & Biological Laboratories. Biotinylated goat anti-rabbit IgG and avidinbiotin-peroxidase complex (ABC Staining System) were purchased from Santa Cruz Biotechnology (CA, USA).
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5

Cell Cycle Analysis by Flow Cytometry

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The cells were treated as indicated. After 48 h treatment, 4 × 106 cells were washed twice with cold PBS containing 1% FBS. After ethanol fixation (at least 12 h at 4°C), cells were washed twice with cold PBS. The pelleted cells were stained by adding PBS containing PI (Sigma-Aldrich) and RNase A (Amersham). Staining was achieved in the dark at 4°C for 3 h prior to flow cytometry analysis using a BD LSR Fortessa flow cytometer, and analyzed with the Tree Star FlowJo (Ashland, OR, USA) software program to model the cell cycle assays. Fluorescence data were collected using a 561 nm laser excitation, and emission was collected using a 610/20 filter. Fluorescence data were obtained from at least 10,000 viable cells per sample.
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6

Nuclear Protein Fractionation and FPLC

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MDA‐MB‐231 cells were washed twice with cold PBS, scraped, and collected by centrifugation at 1500 × g for 5 min. Nuclear and cytoplasmic proteins were extracted using the Nuclear‐Cytosol Extraction Kit (Applygen Technologies, Beijing, China). The supernatant (nuclear fraction) was collected by centrifugation at 13 000 × g for 30 min at 4 °C. The protein concentration was determined using the BCA Pierce protein assay kit (Thermo Fisher Scientific) and MDA‐MB‐231 nuclear proteins (6 mg) were used for the FPLC assay. The proteins were concentrated to 1 mL using a Millipore Ultrafree centrifugal filter apparatus (10 kDa nominal molecular mass limit) and then applied to an 850 × 20 mm Superose 6 size exclusion column (Amersham Biosciences) that was equilibrated with buffer D (20 × 10‐3m HEPES, pH 8.0, 10% glycerol, 0.1 × 10‐3m EDTA, and 300 × 10‐3m NaCl) containing 1 × 10‐3m dithiothreitol and calibrated with protein standards (blue dextran, 2000 kDa; thyroglobulin, 669 kDa; ferritin, 440 kDa; catalase, 232 kDa; bovine serum albumin, 67 kDa; and RNase A, 13.7 kDa; Amersham Biosciences). The column was eluted at a flow rate of 0.5 mL min‐1 and fractions were collected.
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