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The most comprehensive recent data set of this type is by Wayne et al. [ 16] describing whole genome expression levels in 72 genotypes of males and females.
For that purpose, and given that the fold-back precursors for these sequences were already detected in the genome, expression levels were used as a secondary supporting criterion [ 29].
After the alignment of high throughput short sequence reads to the reference genome, expression levels can be quantified in terms of total number of reads that are aligned to the genes.
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Whole-genome expression levels were analyzed by a two-color microarray-based approach.
When the polyploid had a different level of expression than its respective diploid, the AT-genome expression levels were more frequently higher than the A-genome diploid expression levels and the DT-expression levels were more frequently lower than the D-genome diploid expression levels.
To examine the mitochondrial genome expression-level changes across different developmental stages, we plotted the normalized mitochondrial expression level, measured in RPKM*, across all nine datasets and normalized against the dataset size.
The present study provides detailed insight into the response of the leaves of two pairs of rice NILs with contrasting tolerance to drought stress at the whole-genome expression level during the reproductive stage.
However, the use of short reads for the process of measuring genome wide expression levels, an approach called RNAseq, is somewhat dependent on the existence of high quality transcriptome annotations [23], [37], [38], [39].
Similar genome wide expression levels were observed between all tissue types, with an average of 27.57 % of genes displaying no expression (Fig. 4a).
In this study, systemic differences among 100 animals that exhibited diverse responses to PRRSv infection were explored using microarray analysis of whole genome blood expression levels.
Here we analyzed genome wide expression levels in three contrasting phenotypes that represent distinct stages of color transformation in these fish.
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