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10 protocols using odyssey classic imaging system

1

Analyzing Retinal Protein Expression in AION

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We dissected retinae 1 day after AION induction and prepared retinal lysates. We extracted total protein in 1× radioimmunoprecipitation assay buffer (Abcam, Burlingame, CA, USA). For Western blot analysis, equal amount of protein (25 to 50 μg) was resolved by 12% Criterion XT Bis-Tris protein gel electrophoresis and transferred to polyvinylidene difluoride membranes (all from Bio-Rad, Hercules, CA, USA). Membranes were blocked with Odyssey Blocking Buffer (LI-COR, Lincoln, NE, USA) and incubated with primary antibodies against CHOP (mouse, 1:1000, Thermo Fisher Scientific, Waltham, MA, USA), control protein glyceraldehyde 3-phosphate dehydrogenase (GAPDH; rabbit, 1:2000, Cell Signaling, Danvers, MA, USA) or GRP78 (mouse, 1:1000, BD Biosciences, Franklin Lakes, NJ, USA), followed by incubation with IRDye 680-conjugated goat anti-rabbit or IRDye 800-conjugated goat anti-mouse secondary antibodies (LI-COR). We visualized positive bands on immunoblots using the Odyssey Classic Imaging System and performed densitometry analysis using Image Studio software (LI-COR).
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2

Serum Antibody Titration and Tissue Immunoblotting

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Serum antibody titres were determined using LegendPlex (BioLegend), according to the manufacturer’s instructions. For tissue-immunoblots, organs/tissues were harvested from RAG2-deficient B6 mice, rinsed in PBS, and lysed with a Dounce homogenizer in RIPA buffer containing a protease inhibitor cocktail. The crude tissue extracts were centrifuged (104G, 12 min) and the soluble protein extracts were aliquoted and stored at -80°C. The protein concentration was determined using standard Bradford Protein Assay. 35 μg of total soluble protein-extract was run on SDS-PAGE, then blotted on a nitrocellulose membrane. Membranes were incubated in Odyssey blocking buffer (Li-Cor) for 30’ at RT, then incubated o/n at 4°C with 800-fold-diluted sera from scurfy mice injected or not with Treg. Bound immunoglobulin was detected using IRDye® 800CW-labeled Goat-anti-Mouse IgG(1/2a/2b/3)(LiCor, 1h at RT). This antibody also reacts with Igκ and IgΛ. Fluorescence was visualized and quantified using the Odyssey Classic Imaging System and ImageStudio software (Li-Cor).
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3

Western Blot Analysis of Cellular Proteins

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Cell lysates were prepared by washing cells twice with cold PBS and lysing cells in RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5% sodium deoxycholate, 1% NP-40, 0.1% SDS, 1 mM EDTA, protease inhibitors) on ice for 30 min. Lysates were cleared by centrifugation and protein concentrations were determined using the Pierce 660 nm Protein Assay Kit (Thermo Fisher Scientific). Equal amounts of protein were diluted in Laemmli sample buffer, boiled for 5 min and resolved by SDS-polyacrylamide gel electrophoresis. The resolved proteins were then transferred onto nitrocellulose membranes. Membranes were then blocked for 1 h in 5% milk in tris-buffered saline/0.1 % Tween-20 (TBS-T) at room temperature, then probed with the following primary antibodies in 5% milk/TBS-T overnight at 4 °C: SREBP-2 (1:250, BD Biosciences, 557037), p44/42 MAPK (ERK1/2) (1:1000, Cell Signaling Technology, 4695), PARP (1:1000, Cell Signaling Technology, 9542 L), ɑ-Tubulin (1:3000, Calbiochem, CP06) and E-cadherin (1:1000, Cell Signaling Technology, 3195). Primary antibodies were detected using IRDye-conjugated secondary antibodies (1:20,000, LI-COR Biosciences, 926-32211 and 926-32210) and the Odyssey Classic Imaging System (LI-COR Biosciences). Densitometric analysis was performed using ImageJ v1.47 software.
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4

Western Blot Analysis of Caspase-6

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Proteins were transferred to polyvinylidene fluoride membranes after SDS–PAGE using a Bio-Rad trans-blot turbo system. Membranes were blocked with 5% nonfat dry milk in TBS and 0.1% Tween for 1 h prior to incubation with appropriate caspase-6 antibodies (Cell Signaling, catalog nos. 9761 and 9762). Primary antibodies were utilized at dilutions of 1:1000. Secondary antibodies obtained from LiCor were used at dilutions of 1:20000 (IRDye IgG antibodies, catalog nos. 5470S, 5151S, 5257S, and 5366S). Images were both collected and analyzed using a LiCor Odyssey classic imaging system.
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5

Western Blot Analysis of Transfected Cells

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About 21 h after transfection, the 1.5 ml growth medium per well was centrifuged at 1000g for 3 min at 4 °C. Then, 0.5 ml of 4× sample buffer (277.8 mM Tris–HCl, 44.4% v/v glycerol, 4.4% v/v SDS, 0.02% w/v bromphenol blue, 5% v/v β-mercaptoethanol, pH 6.8) was added. The cells in the 6-well plate (catalog no.: 83.3920.005; Sarstedt) were scraped off with a cell scraper, washed two times with PBS by cell pelleting at 1000g for 3 min at 4 °C, and the cell pellet was resuspended in 80 μl 1× sample buffer. Samples were agitated at 95 °C for 10 min and then subjected to SDS-PAGE using a 4% polyacrylamide stacking gel and 8% running gel and blotted to a nitrocellulose membrane (catalog no.: HP40.1; Carl Roth; 0.2 μm pore size). Membranes were washed in PBS and blocked for 1 h with Intercept blocking buffer (catalog no.: 927-70001; Li-Cor). Then, membranes were incubated with primary antibodies diluted in Intercept blocking buffer supplemented with 0.1% v/v Tween-20 overnight at 4 °C. After washing four times with PBS supplemented with 0.1% Tween-20, membranes were incubated with secondary antibodies diluted in Intercept blocking buffer containing 0.1% Tween-20 for 1 h at RT. Thereafter, membranes were washed three times with PBS supplemented with 0.1% Tween-20 and one time with PBS. Bands were detected using the 700 and 800 nm channels of a Li-Cor Odyssey Classic Imaging System.
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6

Western Blot Analysis of Cell Lysates

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Whole cell lysates were prepared by washing cells twice with cold PBS and lysing cells in RIPA buffer (50 mM Tris–HCl pH 8.0, 150 mM NaCl, 0.5% sodium deoxycholate, 1% NP-40, 0.1% SDS, 1 mM EDTA, protease inhibitors) on ice for 30 min. Lysates were cleared by centrifugation and protein concentrations were determined using the Pierce 660 nm Protein Assay Kit (Thermo Fisher Scientific). Equal amounts of protein were diluted in Laemmli sample buffer, boiled for 5 min and resolved by SDS-polyacrylamide gel electrophoresis. The resolved proteins were then transferred onto nitrocellulose membranes. Membranes were blocked for 1 h in 5% milk in PBS/0.1% Tween-20 (PBS-T) at room temperature, and then probed with the following primary antibodies in 5% milk/PBS-T overnight at 4 °C: SREBP2 (1:250; BD Biosciences, 557037), SREBP1 (1:250; Santa Cruz, sc-13551), α-Tubulin (1:3000; Calbiochem, CP06), Actin (1:3000; Sigma, A2066), PARP (1:1000; Cell Signaling Technology, #9542). Primary antibodies were detected using IRDye-conjugated secondary antibodies and the Odyssey Classic Imaging System (LI-COR Biosciences). Densitometric analysis was performed using ImageJ 1.47v software.
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7

Cell Lysis and Protein Extraction

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The cells were collected and washed once with ice-cold PBS and resuspended in modified RIPA lysis buffer containing 50 mM Tris-HCl (pH 7.4), 1 mM EDTA, 100 mM NaCl, 0.1% SDS, 1 x Halt protease and phosphatase inhibitor cocktail, 1 mM PMSF, 1 mM sodium orthovanadate, 1 μg/ml leupeptin, 1 μg/ml pepstatin, and 10 μg/ml aprotinin, for 10 minutes. The lysates were further sonicated in ice-cold water for 4 minutes and then centrifuged at 16,000×gfor 15 minutes at 4°C. Supernatant was collected and protein concentration was quantified using the Pierce BCA Protein Assay kit (Thermo Fisher Scientific) or Bradford reagent (Bio-Rad). Equal amount of sample was resuspended in lx SDS loading dye, boiled at 100°C for 5 minutes, loaded on a 10, 12.5 or 15% SDS-PAGE gel, and resolved electrophoretically at 100V for 1.5 h. After electrophoresis, proteins were transferred to a nitrocellulose membrane at 100V for 2 h. Non-specific binding sites on the membrane were blocked by incubating the membrane in 5% BSA solution for 1 h at room temperature. The membranes were probed with the indicated primary antibody (1: 1000), washed three times for 5 minutes each, followed by incubation with a secondary fluorescence labeled antibody (1:7500). The antibody-bound proteins were detected by LI-COR Odyssey classic imaging system. Band intensity was analyzed using ImageJ software.
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8

Immunoblotting of Bed Bug Salivary Proteins

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Crushed C lectularius salivary gland was mixed with diluted 4× loading buffer (LI-COR), denatured, and separated by SDS-PAGE on 4% to 15% Mini-PROTEAN TGX gels (Bio-Rad) with diluted 10× Tris/glycine/SDS buffer (Bio-Rad) at 5 μg of protein per well. The separated proteins were transferred to PVDF transfer membranes (Thermo Scientific) through a wet transfer process with transfer buffer (20% methanol, 10% Tris-glycine). The membranes were then blocked with Odyssey Blocking Buffer (LI-COR) for 1 hour and incubated overnight with participant serum diluted 1:10 in TBST (Tris-buffered saline [Bio-Rad] plus 0.1% Tween 20 [Fisher Scientific]). Fluorescence-based Western blotting was then performed on the membranes by probing bands with an IRDye 800CW–labeled goat antihuman IgG secondary antibody (LI-COR) diluted 1:7,000 in TBST. The membranes were then dry scanned on an Odyssey Classic Imaging system (LI-COR).
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9

Western Blot Analysis of Transfected Cells

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HepG2 cells were lysed 22 h after transfection by addition of buffer A (82.25 mM Tris-HCl, 32.9% (w/v) glycerol, 2.6% SDS, pH 6.8). The lysate was mixed 1:4 with buffer A with additional 5% β-mercaptoethanol and was heated to 95 °C for 10 min. Proteins were separated on a 12% SDS-PAGE and blotted on a Nitrocellulose membrane (Carl Roth, #HP40.1) using a tank blot system (Bio-Rad, #1703930). The membrane was blocked with blocking buffer, a 1:1 mixture of TBS-T (50 mM Tris, 150 mM NaCl, 0.05% Tween 20 (w/v), pH 7.4) and Odyssey Blocking Buffer (Li-Cor, #927-40000). Membranes were incubated with primary antibodies in blocking buffer and incubated over night at 4 °C. Primary antibodies used were rabbit polyclonal anti-GFP (Thermo Fisher Scientific, #A-11122) diluted 1:2,000 and mouse monoclonal anti-beta-Actin (Cell Signaling, #3700) diluted 1:5,000. The secondary antibodies donkey anti-mouse coupled to IRDye 680RD (Li-Cor, #926-68072) and donkey anti-rabbit coupled to IRDye 800CW (Li-Cor, #926-32213) were diluted 1:10,000 in blocking buffer. The membrane was imaged using an Odyssey Classic Imaging System (Li-Cor).
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10

Western Blot Analysis of Intracellular Signaling

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Cell lysates were prepared by washing cells twice with cold PBS and lysing cells in RIPA buffer (50 mM
Tris-HCl pH 8.0, 150 mM NaCl, 0.5% sodium deoxycholate, 1% NP-40, 0.1% SDS, 1 mM EDTA, protease inhibitors) on ice for 30 min. Lysates were cleared by centrifugation and protein concentrations were determined using the Pierce 660 nm Protein Assay Kit (Thermo Fisher Scientific). Equal amounts of protein were diluted in Laemmli sample buffer, boiled for 5 min and resolved by SDS-polyacrylamide gel electrophoresis. The resolved proteins were then transferred onto nitrocellulose membranes. Membranes were then blocked for 1 hr in 5% milk in tris-buffered saline/0.1 % Tween-20 (TBS-T) at room temperature, then probed with the following primary antibodies in 5% milk/TBS-T overnight at 4 ℃: SREBP-2 (1:250, BD Biosciences, 557037), p44/42 MAPK (ERK1/2) (1:1000, Cell Signaling Technology, 4695), PARP (1:1000, Cell Signaling Technology, 9542L), a-Tubulin (1:3000, Calbiochem, CP06) and E-cadherin (1:1000, Cell Signaling Technology, 3195). Primary antibodies were detected using IRDye-con ugated secondary antibodies and the Odyssey Classic Imaging System (LI-COR Biosciences).
Densitometric analysis was performed using ImageJ 1.47v software.
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