Difference between revisions of "Team:CPU CHINA/Experiments"

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var MTT="<h2>Reagent Preparation</h2>"+
 
var MTT="<h2>Reagent Preparation</h2>"+
 
"<br><br>"+
 
"<br><br>"+
"<h4>The concentration of MTT is 5mg/ml. Weigh MTT 0.5 g, dissolve in 100 ml of phosphate buffer solution (PBS) or culture medium without phenol red, with 0.22 μm filter membrane filtration to remove the bacteria in the solution, store at 4 ℃ and avoid light preservation. Containers are best wrapped in aluminum foil during preparation and preservation.</h4>"+
+
"<h4>(1)The concentration of MTT (Biofoxx, Germany) is 5mg/ml. We prepare this by dissolving 0.5 g of MTT in 100 ml of phosphate buffer solution (PBS) or culture medium without phenol red. </h4>"+
 +
"<h4>(2)Filter the solution with 0.22 μm filter membrane to remove the bacteria, then store it at 4 ℃ (light should be avoided). Containers should be wrapped in aluminum foil during preparation and preservation.</h4>"
 
"<br>"+
 
"<br>"+
 
"<h2>Culturing Cells </h2>"+
 
"<h2>Culturing Cells </h2>"+
"<h4>HepG2 cell (3* 10<sup>4</sup> /mL)s were seeded in 96-well plate according to 100 µL/ well, cultured at 37 ℃ and 5% CO2 constant temperature incubator.</h4>"+
+
"<h4>Seed HepG2 cells (3* 10<sup>4 </sup>/mL) with DEME medium (Gibco, US) in 96-well plate at the amount of 100 µL/ well, culture in a constant temperature incubator (37 ℃, 5% CO<sub>2</sub>).</h4>"+
 
"<br>"+
 
"<br>"+
 
"<h2>Labeling Cells</h2>"+
 
"<h2>Labeling Cells</h2>"+
"<h4>1. For adherent cells, remove the medium and replace it with 100 µL of fresh culture medium. For non-adherent cells, centrifuge the microplate, pellet the cells, carefully remove as much medium as possible and replace it with 100 µL of fresh medium.</h4>"+
+
"<h4>1. For adherent cells, remove the medium and replace it with 100 µL of fresh culture medium. </h4>"+
"<h4>2. Add 20 µL of the 12 mM MTT stock solution (prepared) to each well. Include a negative control of 20 µL of the MTT stock solution added to 100 µL of medium alone.</h4>"+
+
"<h4>2. Add 20 µL of 12 mM MTT stock solution (prepared in advance) into each well. Include a negative control of 20 µL MTT stock solution added into blank 100 µL medium.</h4>"+
"<h4>3. Incubate at 37°C for 4 hours. At high cell densities (>100,000 cells per well) the incubation time can be shortened to 2 hours.</h4>"+
+
"<h4>3. Incubate at 37°C for 4 hours. When cell density is high (>100,000 cells per well) the incubation time can be shortened to 2 hours.</h4>"+
"<h4>4. Add 150 µL of the DMSO solution to each well and mix thoroughly using the pipette.</h4>"+
+
"<h4>4. Add 150 µL of DMSO solution into each well and mix thoroughly using the pipette.</h4>"+
"<h4>5. Incubate the microplate at 37°C for 10 min in a humidified chamber. Longer incubations will decrease the sensitivity of the assay.</h4>"+
+
"<h4>5. Incubate the microplate at 37°C for 10 min in a humidified chamber. Lengthened incubation decrease the sensitivity of the assay.</h4>"+
"<h4>6. Mix each sample again using a pipette and read absorbance at 570 nm as detection wavelength and 630 nm as reference wavelength.</h4>"+
+
"<h4>6. Mix each sample again using a pipette and read its absorbance with 570 nm as the detection wavelength and 630 nm as the reference wavelength.</h4>"+
 
"<br>";
 
"<br>";
  
var qPCR = "<h2>The extraction of RNA</h2>"+
+
var qPCR = "<h3><i>1. Homogenization:</i></h3>"+
"<h3><i>A. Required reagents:</i></h3>"+
+
"<h4>DEPC-treated water (Ambion)、Transzol UP Reagent (Transgen)、Ice cold PBS、Cell scraper、70% ethanol、Isopropyl alcohol.</h4>"+
+
"<h3><i>B. Equipment and supplies:</i></h3>"+
+
"<h4>Refrigerated centrifuge、Microcentrifuge、Micropipettors、Aerosol-barrier tips、Vortex mixer Powder-free gloves、Centrifuge tubes.</h4>"+
+
"<h3><i>C. Safety:</i></h3>"+
+
"<h4>Always use gloves and eye protection. Avoid contact with skin or clothing. Use in a chemical hood. Avoid breathing vapor. </h4>"+
+
"<h3><i>D: Homogenization:</i></h3>"+
+
 
"<h4>Hepg2 cell grown in Monolayer </h4>"+
 
"<h4>Hepg2 cell grown in Monolayer </h4>"+
"<h4>Rinse cell monolayer with ice cold PBS once. Lyse cells directly in a culture dish by adding 1 ml of Transzol UP Reagent per 3.5 cm diameter dish and scraping with cell scraper. Pass the cell lysate several times through a pipette. Vortex thoroughly. The amount of Transzol UP Reagent added is based on the area of the culture dish (1 ml per 10 cm<sup>2</sup>) and not on the number of cells present. An insufficient amount of Transzol UP Reagent may result in DNA contamination of the isolated RNA.</h4>"+
+
"<h4>(1) Rinse the cells with ice cold PBS once. Lyse cells directly in a culture dish by adding 1 ml of Transzol UP Reagent (Transgen, China) per 3.5 cm diameter dish and scrape it with a cell scraper.</h4>"+
"<h3><i>E. PHASE SEPERATION:</i></h3>"+
+
"<h4>(2) Pass the cell lysate several times through a pipette. Vortex thoroughly. The amount of Transzol UP Reagent added is based on the area of the culture dish (1 ml/10 cm<sup>2</sup>) and, not on the number of cells present. An insufficient amount of Transzol UP Reagent may result in DNA contamination of the isolated RNA.</h4>"+
"<h4>Add 0.2 ml of chloroform per 1 ml of Transzol UP Reagent. Cap sample tubes securely. Vortex samples vigorously for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x.g for 15 minutes at 2 to 8℃. Following centrifugation, the mixture separates into lower red, phenolchloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. Transfer upper aqueous phase carefully without disturbing the interphase into fresh tube. Measure the volume of the aqueous phase (The volume of the aqueous phase is about 60% of the volume of Transzol UP Reagent used for homogenization).</h4>"+
+
"<h3><i>2. PHASE SEPERATION:</i></h3>"+
"<h3><i>F. RNA PRECIPITATION:</i></h3>"+
+
"<h4>(1) Add 0.2 ml of chloroform per 1 ml of Transzol UP Reagent. Cap sample tubes securely. Vortex samples vigorously for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 RPM for 15 minutes at 2 to 8℃. </h4>"+
"<h4>Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of Transzol UP Reagent used for the initial homogenization. Incubate samples at 15 to 30oC for 10 minutes and centrifuge at not more than 12,000 x g for 10 minutes at 2 to 4℃. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.</h4>"+
+
"<h4>(2) Following centrifugation, a lower red phenolchloroform phase, an interphase and a colorless upper aqueous phase are visually separated within the mixture. RNA remains exclusively in the aqueous phase. </h4>"+
"<h3><i>G: RNA WASH:</i></h3>"+
+
"<h4>(3) Transfer the upper aqueous phase carefully without disturbing the interphase into fresh tube. Measure the volume of the aqueous phase (The volume of the aqueous phase is about 60% of the volume of Transzol UP Reagent used for homogenization).</h4>"+
"<h4>Remove the supernatant completely. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of Transzol UP Reagent used for the initial homogenization. Mix the samples by vortexing and centrifuge at no more than 7,500 x.g for 5 minutes at 2 to 8℃. Repeat above washing procedure once. Remove all leftover ethanol.</h4>"+
+
"<h3><i>3. RNA PRECIPITATION:</i></h3>"+
"<h3><i>H. REDISSOLVING RNA:</i></h3>"+
+
"<h4>(1) Precipitate the RNA from the aqueous phase by mixing it with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of Transzol UP Reagent used for the initial homogenization. </h4>"+
"<h4>Air-dry or vacuum dry RNA pellet for 5-10 minutes. Do not dry the RNA pellet by centrifuge under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Partially dissolved RNA samples have an A<sub>260</sub>/A<sub>280</sub> ratio < 1.6. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip.</h4>"+
+
"<h4>(2) Incubate samples at 15 to 30℃ for 10 minutes and centrifuge at no more than 12,000 RPM for 10 minutes at 2 to 4℃. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.</h4>"+
"<h3><i>I. SPECTROPHOTOMETRIC ANALYSIS:</i></h3>"+
+
"<h3><i>4: RNA WASH:</i></h3>"+
"<h4>Dilute 1 μl of RNA with 39 μl of DEPC-treated water (1:40 dilution). Using 10 μl microcuvette, take OD at 260 nm and 280 nm to determine sample concentration and purity. The A<sub>260</sub>/A<sub>280</sub> ratio should be above 1.6. Apply the convention that 1 OD at 260 equals 40 µg /ml RNA.</h4>"+
+
"<h4>(1) Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of Transzol UP Reagent used for the initial homogenization. </h4>"+
 +
"<h4>(2) Mix the samples by vortex and centrifugation at no more than 7,500 RPM for 5 minutes at 2 to 8℃. Repeat above washing procedure once. Remove all leftover ethanol.</h4>"+
 +
"<h3><i>5. REDISSOLVING RNA:</i></h3>"+
 +
"<h4>(1) Air-dry or vacuum dry the RNA pellet for 5-10 minutes. (Do not dry the RNA pellet by centrifuge under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility.) Partially dissolved RNA samples have an A260/A280 ratio < 1.6. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip.</h4>"+
 +
"<h3><i>6. SPECTROPHOTOMETRIC ANALYSIS:</i></h3>"+
 +
"<h4>(1) Dilute 1 μl of RNA with 39 μl of DEPC-treated water (1:40 dilution). </h4>"+
 +
"<h4>(2) Using 10 μl microcuvette, take OD at 260 nm and 280 nm to determine the sample concentration and purity. </h4>"+
 +
"<h4>(3) The A260/A280 ratio should be above 1.6. Apply the convention that 1 OD at 260 equals 40 µg /ml RNA. </h4>"+
 
"<h3>Reverse transcription</h3>"+
 
"<h3>Reverse transcription</h3>"+
"<h4>Use Vazyme miRNA 1st Strand cDNA Synthesis Kit (by stem-loop)</h4>"+
+
"<h4>Use Vazyme miRNA 1st Strand cDNA Synthesis Kit (by stem-loop)(Vazyme Biotech, China)</h4>"+
 
"<h4>1. Genomic DNA removal</h4>"+
 
"<h4>1. Genomic DNA removal</h4>"+
 
"<h4>a. The following mixture was prepared in the RNase-free centrifuge tube:</h4>"+
 
"<h4>a. The following mixture was prepared in the RNase-free centrifuge tube:</h4>"+
Line 315: Line 316:
 
"<td style=\"padding-left:200px !important;\"><h4>10 pg-1 μg</h4></td></tr></table>"+
 
"<td style=\"padding-left:200px !important;\"><h4>10 pg-1 μg</h4></td></tr></table>"+
  
"<h4>Gently blow with a pipette to mix.</h4>"+
+
"<h4>Gently blow the mixture with a pipette to mix.</h4>"+
 
"<h4>b. Genomic DNA removal was performed under the following conditions: 42℃ 2 min</h4>"+
 
"<h4>b. Genomic DNA removal was performed under the following conditions: 42℃ 2 min</h4>"+
 
"<h4>2. First strand cDNA synthesis</h4>"+
 
"<h4>2. First strand cDNA synthesis</h4>"+
Line 332: Line 333:
 
"<td style=\"padding-left:200px !important;\"><h4>2 μl</h4></td></tr></table>"+
 
"<td style=\"padding-left:200px !important;\"><h4>2 μl</h4></td></tr></table>"+
  
"<h4>Gently blow with a pipette to mix.</h4>"+
+
"<h4>Gently blow it with a pipette to mix.</h4>"+
 
"<h4>b. First strand cDNA synthesis was performed under the following conditions:</h4>"+
 
"<h4>b. First strand cDNA synthesis was performed under the following conditions:</h4>"+
  
Line 344: Line 345:
  
 
"<h2>qPCR</h2>"+
 
"<h2>qPCR</h2>"+
"<h4>Use Vazyme ChamQ Universal SYBR® qPCR Master Mix</h4><br>"+
+
"<h4>Follow the instruction in <i>Vazyme ChamQ Universal SYBR® qPCR Master Mix</i> (Vazyme Biotech, China).</h4><br>"+
  
"<h2>Homologous recombination</h2>"+
 
"<h4>Use Vazyme ClonExpress II One Step Cloning kit</h4><br>";
 
  
 
var IF = "<h2>Sample preparation: </h2>"+
 
var IF = "<h2>Sample preparation: </h2>"+
"<h4>1.Grow cultured cells on chamber slides overnight, or add appropriate amount of cells to poly-L-lysine coated chamber slides and incubate at least 30 min at 37°C, at the time of fixation cells should be ~50% confluent. </h4>"+
+
"<h4>1.Grow cultured cells on chamber slides overnight. </h4>"+
 
"<h4>2.Rinse cells briefly in PBS. </h4>"+
 
"<h4>2.Rinse cells briefly in PBS. </h4>"+
"<h4>3.Fix cells by incubation with 4% Paraformaldehyde, in PBS for 15 min at room temperature. </h4>"+
+
"<h4>3.Fix cells by incubation with 4% Paraformaldehyde(Servicebio, China), in PBS for 15 min at room temperature. </h4>"+
 
"<h4>4.Rinse three times in PBS, 3 min each. </h4>"+
 
"<h4>4.Rinse three times in PBS, 3 min each. </h4>"+
 
"<h4>5.Add ice-cold acetone and incubate at -20°C for 10 min. </h4>"+
 
"<h4>5.Add ice-cold acetone and incubate at -20°C for 10 min. </h4>"+
Line 358: Line 357:
  
 
"<h2>Sample Blocking:</h2>"+
 
"<h2>Sample Blocking:</h2>"+
"<h4>Block samples in 5% normal serum from same species as secondary antibody in 1% BSA/0.2% Triton X-100/PBS for 1 h at room temperature, or overnight at 4°C.</h4><br>"+
+
"<h4>Block samples in 5% normal serum from same species as secondary antibody in 1% BSA/0.2% Triton X-100/PBS(Sinopharm Chmical Reagent, China) for 1 h at room temperature, or overnight at 4°C.</h4><br>"+
 
 
 
"<h2>Sample staining:</h2> "+
 
"<h2>Sample staining:</h2> "+
 
"<h4>7.Dilute the primary antibody to the recommended concentration/dilution in 1% BSA/0.05% Triton X-100/PBS. </h4>"+
 
"<h4>7.Dilute the primary antibody to the recommended concentration/dilution in 1% BSA/0.05% Triton X-100/PBS. </h4>"+
"<h4>8.Add 200 µl per well (8 wells) to the chamber slides and incubate 2 h at room temperature, or overnight at 4°C. </h4>"+
+
"<h4>8.Add 200 µl/well (8 wells) to the chamber slides and incubate 2 h at room temperature, or overnight at 4°C. </h4>"+
 
"<h4>9. Rinse three times in PBS, 3 min each.<h4>"+
 
"<h4>9. Rinse three times in PBS, 3 min each.<h4>"+
 
"<h4>10. Prepare fluorochrome-conjugated secondary antibody antibodies in 1% BSA/0.05% Triton X -100/PBS according to the recommended manufacturer specification data sheet and add 200 µl per well (8 wells) to the chamber slides. </h4>"+
 
"<h4>10. Prepare fluorochrome-conjugated secondary antibody antibodies in 1% BSA/0.05% Triton X -100/PBS according to the recommended manufacturer specification data sheet and add 200 µl per well (8 wells) to the chamber slides. </h4>"+
 
"<h4>11. Incubate the samples for 1 h at room temperature in dark. </h4>"+
 
"<h4>11. Incubate the samples for 1 h at room temperature in dark. </h4>"+
 
"<h4>12. Rinse three times in PBS, 3 min each. </h4>"+
 
"<h4>12. Rinse three times in PBS, 3 min each. </h4>"+
"<h4>13. Add DAPI solution in 1% BSA/0.05% Triton X -100/PBS, and incubate 15 min at room temperature.</h4>"+
+
"<h4>13. Add DAPI solution (Beyotime, China) in 1% BSA/0.05% Triton X -100/PBS, and incubate 15 min at room temperature.</h4>"+
 
"<h4>14. Rinse three times in PBS, 3 min each.</h4>"+
 
"<h4>14. Rinse three times in PBS, 3 min each.</h4>"+
 
"<h4>15. Coverslip with anti-fade mounting medium and seal slides with nail polish.</h4>"+
 
"<h4>15. Coverslip with anti-fade mounting medium and seal slides with nail polish.</h4>"+
"<h4>16. Take pictures under a fluorescence microscope</h4><br>";
+
"<h4>16. Take pictures under a fluorescence microscope</h4>"+
 +
        "<h4>17. Fluorescence microscopy.</h4>"
  
 
var WB = "<h2>Cell lysis to extract protein </h2>"+
 
var WB = "<h2>Cell lysis to extract protein </h2>"+

Revision as of 09:47, 7 December 2018

Experiments

Molecular Cloning

Transfection

You can click on the figure to see the protocol.

Characterization

You can click on these arrows to read the details of our experiments.

You can click here to see our Promoter.