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10 protocols using x omat ar

1

Northern Blot Analysis of Plant Viruses

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For northern blot analysis, total RNA was extracted from leaf tissues as described previously [37 (link)]. Total RNA (5 µg) was separated on 1% formaldehyde agarose gels, transferred to positively-charged nylon membranes (Roche Diagnostics, Mannheim, Germany), and probed with digoxigenin-labeled specific RNA probes for the RNA1 and RNA2 3′-untranslated region of TRV (6548–6789 nt of RNA1 and 1860–2101 nt of RNA2), and for the 3′-end region of PVX (5875–6403 nt of PVX cDNA sequence in pgR107 vector). For tissue blot hybridization, fresh cross-sections of four non-inoculated leaf petioles or stems were squash blotted on positively-charged nylon membranes (Roche Diagnostics, Mannheim, Germany), and blots were hybridized with the digoxigenin-labeled RNA probes mentioned above. The hybridization conditions used were those recommended by the manufacturer (DIG Application Manual for Filter Hybridization, Roche Diagnostics, Mannheim, Germany). Membranes were exposed to X-ray film (X-Omat AR, Kodak, Rochester, NY, USA) and developed following a conventional photographic process.
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2

Determining Chromosomal Insertions in Gmm

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To determine the number of chromosomal insertions, genomic DNA from tetracycline-treated Gmm females and normal Gmm individuals were restricted with HindIII endonuclease, electrophoresed on 1% agarose gel in 1× TBE buffer, and transferred to a positively charged nylon membrane according to Southern protocol [68] (link). The membrane was hybridized at 55°C with 350 ng of a 569 bp probe corresponding to part of the wsp gene labeled with the Gene Images Alkphos Direct labeling system (GE Healthcare, Little Chalfont, UK) using the random primer method following manufacturer protocols. Signal detection was performed using CDP-star followed by exposure to autoradiographic film (X-OMAT AR, Kodak). The absence of cytWol from the tetracycline-treated Gmm DNA was confirmed by a PCR assay, which resulted in only a single 16S rRNA amplification product originating from the chromosomal insertions [45] (link).
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3

Northern Blot Analysis of FOSL1 mRNA

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Total RNA was isolated using Tri-Reagent (Sigma-Aldrich) from each of the cell lines by our published methods (10 (link)). RNA was loaded at 15 μg per lane and separated on a standard Northern gel. After transfer to a nylon membrane (Gene Screen Plus, Perkin Elmer, Boston, MA) the membranes were hybridized with 32P-labeled FOSL1 cDNA. After hybridization and washing, the Northern blots were wrapped and exposed to Kodak film (Kodak X-OMAT AR). The FOSL1 mRNA in each lane/cell line were analyzed either visually or scanned and analyzed with Image J software (28 (link)).
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4

Radiographic Assessment of Bone Metastases

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Animals were anesthetized deeply, then x-rayed in a prone position against the film (22×27 cm2 X-Omat AR, Eastman Kodak Co., Rochester, NY) and exposed with X-rays at 35 KVP for 6 s using a Faxitron radiographic inspection unit (43855A; Faxitron X-ray Corporation, Buffalo Grove, IL) as described [17] (link). The radiographs were scanned and the area of osteolytic lesions was measured using NIH Image 1.62 and the results were expressed in square millimeters. The number of bone metastases was also counted in bilateral femurs and tibiae.
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5

Analyzing Protein Expression via Western Blot

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A protocol of a pre�ious study was used for the preparation of cell lysates (14) In brief, the proteins (30 µg) were resol�ed using 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE; Protogel, Atlanta, GA, USA) and transferred onto poly�inylidene difluoride nitrocellulose membranes (EMD Millipore, Billerica, MA, USA). The filters were incubated at room temperature for 2 h in 50 mm Tris-HCl (pH 7.4), 150 mm NaCl, 0.1% (�/�) Tween 20, 0.5% (w/�) bo�ine serum albumin (TBST/BSA) and then overnight at 4˚C on a shaker with the rabbit monoclonal anti-GAPDH (ab181602) and anti-CTGF (ab6992) antibodies (1:1,000 in TBST/BSA; Abcam, Cambridge, UK). The membranes were washed twice with TBST and incubated for 2 h with the horseradish pero�idase-conjugated secondary antibody (1:20,000 in TBST/BSA). Following the final washes, the signals were visualized with Enhanced Chemiluminescence Western Blotting Detection Reagent (GE Healthcare Life Sciences) and autoradiographic film (X-Omat AR; Kodak, Rochester, NY, USA). Densitometric analysis using ImageQuant software was performed following digital scanning (Odyssey ® Fc; Agfa-Ge�aert, Mortsel, Belgium).
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6

Southern Blot Analytical Protocol

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For Southern blot analysis, approximately 5 to 15 µg of genomic DNA, extracted as previously reported, were digested with specific restriction enzymes, were separated on a 1% (wt/vol) agarose and Tris-acetate-EDTA gel and were blotted onto a Hybond NX membrane (Amersham Biosciences, Milano, Italy). Digoxygenin (DIG)-labeled specific probes were generated by PCR with specific primers, using genomic or plasmid DNA as template, and were used for overnight hybridization at 65°C. The PCR reactions were performed in a volume of 25 µl, using DIG-11-dUTP (Roche, Mannheim, Germany), and consisted of a denaturation step at 94°C for 2 min, followed by 35 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C for 2 min. Southern hybridization and detection of the DIGlabeled probes were performed according to manufacturer's instruction. Membranes were exposed to X-ray film (X-Omat AR, Kodak, Rochester, NY, U.S.A.) for approximately 1 to 3 h.
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7

SDS-PAGE Western Blot Analysis

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After each treatment, CHO-K1/A5 cells were washed with M1 and lysed at 4 • C during 1 h with cell lysis buffer (20 mM HEPES; 10 mM EGTA; 5 mM ␤-glycerol phosphate, 1% Nonidet P-40; 2.5 mM MgCl 2 ) containing protease inhibitors (2 g/ml leupeptin; 1 g/ml aprotinin; 1 g/ml pepstatin; 0.1 mM PMSF). Proteins (40 g) were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) on 10% polyacrylamide gels and subsequently transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, Bedford, MA, USA). Membranes were blocked and probed with primary antibodies overnight at 4 • C followed by incubation with the corresponding secondary antibodies at room temperature for 2 h. Immunoreactive bands were detected by enhanced chemiluminescence reagent (ECL, Amersham Biosciences) using standard X-ray film (Kodak X-Omat AR).
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8

Serum IGFBP3 Quantification by Ligand Blot

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Serum IGFBP3 levels were measured by ligand blot. Two microlitres of serum were diluted in sample buffer and boiled for 2 min at 90°C and loaded on to 1% SDS-12.5% polyacrylamide gels, and proteins were separated by electrophoresis under nonreducing conditions. Proteins were transferred onto nitrocellulose sheets (HybondTM-C extra, Amersham, UK). The membranes were dried and blocked for 1 h with 5% nonfat dry milk, 0.1% Tween (Sigma-Aldrich), in Tris-buffered saline. Membranes were probed overnight at 4°C with 125I-labelled IGF-I (1.5 × 106 cpm/mL). The nitrocellulose sheets were then washed, dried, and exposed at −80°C to X-ray film (Kodak X-Omat AR, Eastman Kodak, Rochester, NY, USA). The film signals were quantified by densitometry using a PC-Image VGA24 program for Windows. The density of the IGFBP3 band in each lane was expressed as the percentage of the mean density of sera from control rats.
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9

Quantitative Analysis of GLUT4 in Adipocytes

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Adipocytes were homogenized by using a Dounce homogenizer in a buffer containing 10 μg/ ml aprotinin, 1 mM EDTA, 20 mM HEPES (pH 7.4), 5 μg/ml leupeptin, 1 mM phenylmethylsulfonyl fluoride, and 0.25 mM sucrose. PM fractions were prepared as described previously (27) .
Western blot analysis PM fractions prepared from aliquots of adipocyte homogenates were separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then transferred onto a Hybond-enhanced chemiluminescence (ECL) filter (GE Healthcare Life Sciences). The separated proteins transferred onto the filter were incubated for 1 h with anti-GLUT4 rabbit antibody (1:1000, carboxy-terminal polypeptide [27] ). After incubating with a horseradish peroxidase-conjugated anti-rabbit immunoglobulin-G antibody (1:2500; GE Healthcare Life Sciences), the immune complexes were detected on X-ray film (Kodak X-Omat AR; Eastman-Kodak Co., Rochester, NY) by using an ECL detection system (GE Healthcare Life Sciences). The blots on the film were quantified using the National Institutes of Health Image program (http://rsb.info.nih.gov/nih-image/).
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10

Quantifying IGFBP-3 Levels via Ligand Blot

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Serum concentrations of IGFBP-3 were measured by ligand blot. Two μl of serum were diluted in sample buffer and boiled 2 min at 90°C, loaded onto 1% SDS-12.5% polyacrylamide gels, and electrophoresed under non-reducing conditions. Proteins were transferred onto nitrocellulose sheets (HybondTM-C extra, Amersham, UK). The membranes were dried and blocked for 1 h with 5% non-fat dry milk and 0.1% Tween (Sigma), in Tris-buffered saline. Membranes were probed overnight at 4°C with 125I-labelled IGF-I (1.5 x 106 cpm/ml). The nitrocellulose sheets were then washed, dried and exposed at -80°C to X-ray film (Kodak X-Omat AR, Eastman Kodak, Rochester, NY, USA) and to two intensifying screens for 1–4 days according to the signal obtained. The film signals were quantified by densitometry using a PC-Image VGA24 program for Windows. The density of the IGFBP-3 band in each lane was expressed as the percentage of the mean density of sera from its respective control rats.
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