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Sigma p8340

Manufactured by Merck Group
Sourced in Germany

Sigma P8340 is a lab equipment product. It is a buffer solution used in various biochemical and cell culture applications.

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5 protocols using sigma p8340

1

Mitochondrial Hydrogen Peroxide Quantification

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Approximately 50 mg of liver tissue was homogenized in 1 ml of homogenization buffer containing 25 mM Hepes pH7.4, 1 mM EDTA, 0.25 M sucrose, 2 mM MgCl2, 1 μM butylated hydroxytoluene (BHT), 1:200 dilution of Sigma P8340 and 1 μM diethylenetriaminepentaacetic acid (Sigma-Aldrich). The homogenates were centrifuged at 500 × g for 5 min to pellet nuclei and debri. The resultant supernatant was centrifuged at 10,000 × g for 10 min at 4 °C to obtain mitochondria. The pellets were resuspended in 150 μl homogenization buffer. About 20 μL solution was saved for measuring protein concentration.
Mitochondrial H2O2 was detected using Amplex Red assay as described39 (link). The working solution was prepared using 100 μL of 10 mM Amplex Red reagent (Thermo Fisher Scientific), 2 μL of 1000 U/ml horseradish peroxidase (HRP) and 10 ml of 50 mM potassium phosphate (pH7.7) with 0.5 mM diethylenetriaminepentaacetic acid (Sigma-Aldrich). 50 μL of sample or standard was pipetted into 96 plates, followed by addition of 50 μl of the Amplex Red reagent/HPR working solution. The reaction mixture was protected from light and incubated at room temperature for 30 min. The fluorescence was measured with excitation in the range of 530–560 nm and emission at 590 nm. Mitochondrial H2O2 levels were normalized to protein levels.
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2

Optimized Organoid Fixation and Labeling

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1275-Iodo-2′-deoxyuridine (127IdU) (Fluidigm 201127) was added directly to organoid culture media to a final concentration of 25 μM and incubated at 37 °C for 30 mins before fixation to identify cells in S-phase14 (link). 5 mins before fixation, protease and phosphatase inhibitors (Sigma P8340/Sigma 4906845001) were added to organoid cultures to preserve cell signalling during fixation8 (link). As dissociation of live tissue alters cellular states41 (link) including PTMs8 (link), all organoids were fixed in 4% PFA (Thermo J19943K2) for 60 mins at 37 °C to preserve cell-signalling. (Note: during method optimisation, we also trialled alternative fixatives such as Glutaraldehyde (0.2%, 1%, 2.5%), Ethanol (5%, 10%), and Glyoxal (pH 4.0, pH 5.0), but concluded that 4% PFA was optimal. 1.6% PFA can also be used but we encourage users to test a range of PFA for their specific antibody panel.) Following fixation, organoids were washed ×2 with PBS and incubated in 250 nM 194/8Cisplatin (Fluidigm 201194/8) in PBS for 10 mins on a rocker to stain dead cells15 (link). During optimisation we found this condition yields strong 194/8Pt staining with a wide dynamic range suitable for efficient dead cell removal in silico. Organoids were then washed ×2 with PBS to remove residual Cisplatin. Fixed organoids were subsequently dissociated for single-cell analysis immediately or stored at 4 °C.
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3

Encapsulin Protein Extraction Protocol

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Cells were harvested between 24 and 48 h post transfection. Cells were lysed with M-PER Mammalian Protein Extraction Reagent (Pierce Biotechnology) containing a mammalian protease inhibitor cocktail (SIGMA P8340, Sigma-Aldrich) according to the protocol of the manufacturer in all experiments using FLAG-tagged encapsulins. For lysis of cells expressing StrepTagII-modified encapsulins, cells were resuspended in Buffer W (150 mM NaCl, 100 mM Tris-Cl, pH 8.0) and exposed to four freeze–thaw cycles in LN2. After spinning down cell debris at 10,000 × g for 15 min, cell lysates were kept at 4 °C for downstream analyses. Protein concentrations of lysates were determined by measuring OD at 280 nm.
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4

Transfection and Iron Loading in HepG2 Cells

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Low-passage-number HepG2 (ECACC: 85011430) cells were cultured in DMEM/F-12 with 10% FBS and penicillin–streptomycin at 100 μg/mL at 37 °C and 5% CO2. Cells were transfected with Lipofectamine 3000 Transfection Reagent (Invitrogen) according to the manufacturer’s protocol. To express the combination of QtIMEFP2AQtEncFLAG and Zip14, 95% of the total DNA amount encoded the QtIMEFP2AQtEncFLAG, and 5% of the total DNA amount encoded Zip14. To express the combination of QtEncFLAG and DD-mScarlet-I-QtSig, 65% of the total DNA amount encoded the shell, and the remaining 35% coded the fluorescent cargo. Cells were supplemented with medium containing ferrous ammonium sulfate (FAS, Sigma-Aldrich, Darmstadt, Germany) at the indicated concentrations 24 h after transfection to facilitate iron loading. For protein-expression analysis, cells were harvested 48 h after transfection and lysed with mammalian protein extraction reagent M-PER (Pierce Biotechnology, Waltham, MA, USA) containing a mammalian protease inhibitor cocktail (SIGMA P8340, Sigma-Aldrich, Darmstadt, Germany) according to the manufacturer’s protocol. After spinning down the cell debris at 14,000× g for 15 min, the cell lysates were incubated at 4 °C for subsequent analyses. Protein concentrations in the lysates were determined by OD measurement at 280 nm.
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5

Optimized Organoid Fixation and Labeling

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1275-Iodo-2′-deoxyuridine (127IdU) (Fluidigm 201127) was added directly to organoid culture media to a final concentration of 25 μM and incubated at 37 °C for 30 mins before fixation to identify cells in S-phase14 (link). 5 mins before fixation, protease and phosphatase inhibitors (Sigma P8340/Sigma 4906845001) were added to organoid cultures to preserve cell signalling during fixation8 (link). As dissociation of live tissue alters cellular states41 (link) including PTMs8 (link), all organoids were fixed in 4% PFA (Thermo J19943K2) for 60 mins at 37 °C to preserve cell-signalling. (Note: during method optimisation, we also trialled alternative fixatives such as Glutaraldehyde (0.2%, 1%, 2.5%), Ethanol (5%, 10%), and Glyoxal (pH 4.0, pH 5.0), but concluded that 4% PFA was optimal. 1.6% PFA can also be used but we encourage users to test a range of PFA for their specific antibody panel.) Following fixation, organoids were washed ×2 with PBS and incubated in 250 nM 194/8Cisplatin (Fluidigm 201194/8) in PBS for 10 mins on a rocker to stain dead cells15 (link). During optimisation we found this condition yields strong 194/8Pt staining with a wide dynamic range suitable for efficient dead cell removal in silico. Organoids were then washed ×2 with PBS to remove residual Cisplatin. Fixed organoids were subsequently dissociated for single-cell analysis immediately or stored at 4 °C.
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