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The reliability of such tools as well as they performance are strictly related to accurate gene expression determination which could be affected by sample handling and storage.
Database search engines can be instructed to identify peptides with a set of specified modifications, including those introduced by sample handling and those present in vivo.
To minimize changes in gene expression induced by sample handling and processing, whole-blood samples (2.5 ml) were collected in PAXgene RNA stabilization tubes (Qiagen Inc., Valencia, CA) and frozen at −80°C.
Developing a microarray-based gene expression assay that does not rely on globin reduction or other methods of sample fractionation, such as the isolation of PBMCs or other cell types from the blood, should reduce sample variability introduced by sample handling and preparation.
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These factors may affect biomarker performance due to DNA degradation by sample handling, specially freezing delays and blood conservation.
In this study, the number of indeterminate results, which can be greatly affected by sample handling, was very low, and malnutrition did not appear to be a significant factor.
We used several sets of replicate samples to analyze the reproducibility of our RNA isolation procedure and the variability in total RNA content introduced by sample handling during water collection, filtering, and on-board storage.
Taken together, these data indicate that experimental variability was determined largely by sampling location, and not by sample handling, RNA isolation, or microarray hybridizations.
This normalization removed trends introduced by sample handling, sample preparation, HPLC, mass spectrometry, and possible total protein differences.
Three SMVs were developed from these studies that typify blood components affected by sample handling: complement (4 proteins, primarily C3 and its proteolytic fragments), cell contamination (30 intracellular leukocyte proteins released through cell lysis), and platelet contamination (16 proteins released through activation or lysis) (Additional file 4).
It was demonstrated that the off-line measured drop size distributions are representative for the conditions in the bioreactor and are not altered by sample handling.
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