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We also provide correction factors based on our model for increasing accuracy of transcript quantification in existing samples prepared at standard temperatures.
As we did not have access to the tissue samples used for the RNA-seq analysis, we assessed transcript levels in existing samples of RNA from shoot, root, grain and spike tissues in the tetraploid (durum) wheat cv.
One method would be to use real sequence data in existing samples, but detecting autozygosity in sequence data given current small samples, low pass coverage, and high error rate estimates (e.g., 1-3% in the thousand genomes data; [ 29]) poses a substantial problem in accurately estimating autozygosity.
In order to investigate the potential interaction between Progranulin and SLPI, mucosal and serum levels as well as gene expression levels of Progranulin were analyzed retrospectively in existing samples and tissue specimens in relation to H. pylori status and SLPI expression levels published previously [ 20].
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The basic idea of the method was to use clusters of environmental covariates to approximate types of soil variations, and check the occupancy of the existing samples in centroids of environmental clusters.
All studies in tissues were from existing samples already collected and deidentified and were therefore considered exempt.
Samples from 29 carriers of known mutations in one of the regions of the BRCA1 and BRCA2 genes that contain the Ashkenazi founder mutations were obtained from existing samples in the Diagnostic Molecular Pathology laboratory at the Peter MacCallum Cancer Centre.
In addition, it demonstrates the difficulty studies based on existing samples may have in locating inactive participants for re-consent.
The chosen level of Tween-20 does not interfere with assay performance (Supplementary Fig. 4), and therefore this post-collection mitigation strategy is suggested for use across a wide range of polypropylene tubes and for existing samples already in long-term storage.
These results in combination with the simple collection procedure, the stability of the DNA and the straightforward handling and storage requirements for blood spots enable large-scale methylome-wide investigations in new and existing sample collections for a large set of phenotypes.
A decade later, several EPA officials concluded after a study in Chicago that the existing sampling protocol "systematically misses the high lead levels and potential human exposure". That was especially true where construction or other activity had disturbed lead pipes.
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