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The amount of nptII transcript was determined for two to three plants/calli of each line in several technical replicates.
In this section, we apply our method to a publicly available transcriptional profiling data set comparing several technical replicates of a liver and kidney RNA source [ 5].
Thus, the SWATH method clearly outperformed the DDA approach for the reproducible identification of JYEBV+ HLA class I peptides across several technical replicates.
Most of our experiments were carried out using nuclei from 2.5 × 105 cells per DNaseI digestion aliquot, providing sufficient DNA for several technical replicates.
When such data was unavailable, we generated a reference set by pooling high-confidence protein identifications from several technical replicates of our MS/MS experiment e.g. human data (Section 2.3.4).
Another advantage of using pools is the ability to perform several technical replicates (quadruplicates in the current study), which is impossible with individual tissue given limitations of both tissue and money.
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Also included were several technical replicate samples created from a homogeneous pool containing a small amount of all study samples.
Also included were several technical replicate samples created from a homogeneous pool containing a small amount of all samples considered in the study.
This series of runs (13 in total) also included minor modifications to the sample preparation (e.g. protease digestion conditions and length of LC separation) and several biological and technical replicates.
A quantitative experiment usually comprises several technical or biological replicates [39].
These can be addressed using an experimental design that incorporates several technical and biological replicates to account for variations at two levels, within gels and within samples, respectively [ 18- 20].
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