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7 protocols using stain free imaging system

1

Mitochondrial Protein Expression Analysis

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Whole cell lysates were collected using NP-40 or RIPA buffer with protease inhibitor cocktail (ThermoFisher Scientific, NY, #78443). 30mg total protein was separated by SDS–PAGE using Any kD™ Mini-protean TGX stain-free™ precast gels (BioRad, CA, #4568123), and transferred to PVDF membranes using the Trans-Blot Turbo™ Transfer System (BioRad, CA, #1704155). Membranes were incubated overnight with antibodies against DGUOK (Santa Cruz, #sc-398093, 1:200), HSP90β (Abcam, #ab32568, 1:100000), MT-ATP8 (Santa Cruz, #sc-84231, 1:200), cytochrome b (Santa Cruz, #sc-11436, 1:200), ND6 (Santa Cruz, #sc-20510, 1:200), MTCO1 (abcam, #ab14705, 1:1000), oxidative phosphorylation antibody cocktail (UQCRC2, ATP5A, MTCO1) (Abcam, #ab110413, 1:250), PGC1 alpha (Abcam, #ab77210, 1:400), SOD2 (Abcam, #13533, 1:5000), PINK1 (Abcam, #23707, 1:500) or Acetyl lysine (Abcam, #ab190479, 1:500) at 4°C. HRP-conjugated secondary antibodies were used at a dilution of 1:2000. Protein levels were calculated using BioRad stain-free Imaging System and were normalized to total protein using Image Lab software from BioRad. Immunoprecipitation was performed using Catch and Release® V2.0 kit (EMD Millipore, CA, #17-500) following the manufacturer’s directions.
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2

Cell-Free Synthesis and Characterization of Fatty Acid-Modifying Enzymes

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pEU-ufaO was generated by cloning the ufaO coding region into pEU to produce an N-terminally hexahistidine-tagged protein (His6-ufaO and His6-FufM). Synthesis of both UfaO and FufM was achieved in a wheat germ cell-free extract using published translation conditions (61 (link)). The fatty acid modification reaction was run concurrently with the translation reaction by adding ∼3 mm phospholipid substrate, prepared as described above, to the reaction. The phospholipid substrate was purified from a ΔufaO strain (for the 9M5-FuFA synthesis assay) and a ΔchrR strain (for the FufM assay) to generate phospholipid lysosomes containing putative enzyme substrates and quantified as above (51 (link)). As determined by SDS-PAGE imaging with a Bio-Rad stain-free imaging system (61 (link)), the UfaO reaction contained ∼60 µm UfaO; however, FufM concentration could not be calculated this way as it ran concurrently with other proteins in the wheat germ cell-free system.
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3

Digoxin Affects ApoB Synthesis in iPSC-Derived Hepatocytes

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iPSC–derived hepatocytes (day 20) and undifferentiated iPSCs were treated with DMSO or digoxin (310 nM) overnight. Cells were then incubated for 30 minutes with methionine free DMEM medium before labeling for 60 mins with [35S]-Met ± digoxin (310 nm). Immunoprecipitation of cell lysates was performed using anti-ApoB (MabTech LDL 17/20) and anti-FLAG M2 antibody (SIGMA). After SDS-PAGE using a 4–15% acrylamide gradient, gels were exposed to a phosphorimager screen and developed using a FLA 9000 Typhoon Storage Phosphorimager (GE Healthcare). For western blots iPSC–derived hepatocytes (day 20) were treated between 8 – 24 hours, depending on the experiment, with DMSO, cycloheximide (100 μM), digoxin (310 nM), proscillaridin (310 nM), MG132 (10 μM), or combinations of these drugs. Protein concentration was determined by BCA assay (Bio-Rad) and 30 μg of protein separated by SDS-PAGE using Any kD Mini-protean TGX stain-free precast gels (BioRad, CA, #4568123), and transferred to PVDF membranes using the Trans-Blot Turbo Transfer System (BioRad, CA, #1704155). Membranes were probed with anti-ApoB (MabTech LDL 17/20) and detected using HRP–conjugated secondary antibodies. Protein levels were calculated using the stain-free Imaging System (Bio-Rad) and were normalized to total protein using Image Lab software (Bio-Rad).
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4

SDS-PAGE Analysis of Intestinal Alkaline Phosphatase

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After being isolated using FPLC, the protein fractions containing weaned porcine jejunal IAP were denatured by heating them at 100 °C for 5 min with the addition of 2-mercaptoethanol. The resulting denatured proteins were loaded onto Mini-PROTEAN TGX Stain-Free Precast Gels (Bio-Rad Laboratories, Hercules, CA, USA) in 20 µL solutions containing 0.39–4.27 µg of protein. The jejunal IAP protein bands were separated using the SDS-PAGE electrophoresis and photographed with stain-free imaging system (Bio-Rad Laboratories, Hercules, CA, USA). The molecular weights of the target IAP protein bands were estimated using Image Lab (v5.0, Bio-Rad Laboratories, Hercules, CA, USA).
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5

Quantitative Analysis of RadA Protein

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Before transfer, total proteins loaded into the gel were detected by fluorescence with a stain-free imaging system (Bio-Rad). Intensity of protein bands was quantitated by Image Quant software and compared to a reference (WT) (36 (link)) to normalize data to total protein in each condition: normalization factor = total WT protein/total P15 protein. The stain-free blot was also analyzed to confirm the transfer quality for each condition. Then, the proteins visualized by chemiluminescence were quantitated to obtain the volume (intensity), and this volume was normalized as follows: normalization volume = volume × normalization factor. After normalization, the percentage of RadA protein was the result of the indicated volume/referenced volume (WT).
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6

Production and Analysis of Pc_GH1 Protein

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Example 10

The T. reesei strain expressing the gene encoding Pc_GH1 was cultivated in 20 l fermentor The soluble protein concentration in the fermentor samples was quantified after precipitation with equal volume of 10% trichloroacetic acid for 0.5 h at 4° C. The protein pellet was redissolved in Lowry buffer A (20 g Na2CO3, 4 g NaOH) and the soluble protein concentration was measured with BioRad DC kit according to manufacturer's instruction and using bovine serum albumin as standard. After 144:53 h cultivation, the total protein concentration was 14 g/l. The soluble protein composition in fermentation samples, taken at different time points (time-points (h:min) 0:15, 20:23, 44:18, 68:20, 92:20, 121:08 and 144:53) was analysed with SDS-PAGE using 4-20% BioRad Criterion Stain Free gradient Gels and BioRad Stain Free Imaging system. The Pc_GH1 protein was found to the major component in all the fermentor samples (FIG. 13).

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7

Mitochondrial Protein Expression Analysis

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Whole cell lysates were collected using NP-40 or RIPA buffer with protease inhibitor cocktail (ThermoFisher Scientific, NY, #78443). 30mg total protein was separated by SDS–PAGE using Any kD™ Mini-protean TGX stain-free™ precast gels (BioRad, CA, #4568123), and transferred to PVDF membranes using the Trans-Blot Turbo™ Transfer System (BioRad, CA, #1704155). Membranes were incubated overnight with antibodies against DGUOK (Santa Cruz, #sc-398093, 1:200), HSP90β (Abcam, #ab32568, 1:100000), MT-ATP8 (Santa Cruz, #sc-84231, 1:200), cytochrome b (Santa Cruz, #sc-11436, 1:200), ND6 (Santa Cruz, #sc-20510, 1:200), MTCO1 (abcam, #ab14705, 1:1000), oxidative phosphorylation antibody cocktail (UQCRC2, ATP5A, MTCO1) (Abcam, #ab110413, 1:250), PGC1 alpha (Abcam, #ab77210, 1:400), SOD2 (Abcam, #13533, 1:5000), PINK1 (Abcam, #23707, 1:500) or Acetyl lysine (Abcam, #ab190479, 1:500) at 4°C. HRP-conjugated secondary antibodies were used at a dilution of 1:2000. Protein levels were calculated using BioRad stain-free Imaging System and were normalized to total protein using Image Lab software from BioRad. Immunoprecipitation was performed using Catch and Release® V2.0 kit (EMD Millipore, CA, #17-500) following the manufacturer’s directions.
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