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The fractional cycle number at which the fluorescence passes the fixed threshold (CT values) was used for quantification by using a comparative CT method.
The fractional cycle number at which the fluorescence passes the threshold (Ct values) was used for quantification by using a comparative Ct method.
Stable isotope labeling with amino acids in cell culture (SILAC) is an optimal method for accurate quantitative proteomics and the use of SILAC has been expanded for tissue proteome quantification by using a mix of multiple SILAC-labeled cell lines as internal standards (super-SILAC) [ 15- 17].
The starting point of our process is a bead-based normalisation of genomic DNA (gDNA), a step that replaces quantification by using a defined amount of DNA-binding beads to enforce a reproducible, input DNA quantity while also removing possible contaminants such as salts and proteins.
The purified DNA, 100 ng of genomic DNA for each sample, was used for global DNA methylation quantification by using a MethylFlash Methylated DNA Quantification Kit (Colorimetric, Epigentek, NY) added to an ELISA plate where the methylated fraction of DNA was quantified using 5-deoxy-methyl-cytidine specific antibodies.
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In advance to the evaluation, we established a real-time PCR quantification method by using a LightCycler system.
The effects of Tv6 on the autophagy flux was studied by two different methods: LC3II quantification and by using a RFP/GFP LC3 tandem probe that allows the microscopic visualization of autophagosomes and autolysosomes.
Quantification was done by using a morphometric grid.
Absolute copy number quantification was performed by using a standard miR30a probe at different dilutions (Additional file 4: Figure S3A and Figure S3B).
Identification and quantification of carbamates was performed by using a gas chromatography-triple quadrupole mass spectrometry (GC-QqQ-MS) system in multiple reaction monitoring (MRM) acquisition.
Quantification of bands was done by using a Bio-imaging analyzer LAS 1000 with Image Gauge Ver. 3.4X software (Fuji film).
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