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Hence, absolute quantification via FI-ICP-MS should be considered as challenging because total element concentrations are measured and the accuracy depends on background, clean up steps, labelling conditions and labelling degree.
All cDNA clean up steps were performed using Agencourt AMPure XP beads (Beckman Coulter) and a magnetic stand (Agencourt Bioscience Corporation).
Advantages of pyrosequencing are that it is more sensitive than Sanger sequencing (5% versus 6.6% in our cohort) and the amount of work is lower compared to Sanger sequencing hence no clean up steps of the PCR-products is needed [ 34, 40] but result interpretation is more prone to errors.
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Eighteen experimental factors were considered; 7 related with the extraction and clean up step, 8 with the PTV injection step and 3 factors related with the derivatization step.
A further clean up step was performed after 5-mC IP using the MinElute PCR purification kit (Qiagen).
The original trial run also identified the need for a streamlined normalization and clean up step of PCR product prior to library preparation as there was a large difference in reads produced between samples likely due to amplification bias leading from differences in input DNA (Additional file 1: Fig S1).
The results showed that the method was satisfactory in terms of selectivity and reproducibility with a cleaner chromatogram without any clean up step.
The concentrates were then adjusted to about 2 mL using the rotary film evaporator (Buchi Ratovapor R-210, USA) at 35 °C, and made ready for silica clean up step.
For microarray analysis of sorted populations, a further clean up step was performed using RNeasy Minelute columns (Qiagen).
If the main problem is that your system is running slowly and you have unused programs on board, you might try some simpler clean-up steps before resorting to reformatting the drive.
Their determination requires extraction and clean-up steps, prior to detection, to reach low concentration levels.
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