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Biological replication would be necessary to conclude that the expression differences are inherent differences between leaf and bud rather than simply differences between the particular leaf RNA pool and the particular bud and bud' RNA pools prepared for this experiment.
The difference in homoeolog expression was not significantly different (T test) between leaf and bud tissue, except that AT homoeolog expression was significantly higher in leaves for G. barbadense (P = 1.1024 × 10−10).
If our goal was to describe differentially expressed genes between leaf and bud, we would have a large list of putatively, differentially expressed genes (Table 2); however, in this particular case, we can only claim that these genes were differentially expressed between the two amplified RNA samples considered in our experiment.
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(Again note that these are differences between our RNA pools rather than inherent expression differences between general leaf and bud tissues).
Finally, if we test for expression differences between the leaf RNA pool and each of the bud RNA pools (bud and bud'), many genes were found to be consistently differentially expressed between bud vs. leaf and bud' vs. leaf, as seen by the high correlation among the most significant p-values.
After removal of these contaminants, a total of 14,768 and 12,264 sRNA sequences, with sizes between 15 and 30 nucleotides, remained for the leaf and bud samples.
Leaf and bud tissues were harvested for DNA extraction when plants began to flower.
For strains with both leaf and bud data, only the leaf data was used, resulting in data for 140 different Arabidopsis strains.
Buds in the axils (angle between leaf and stem) of the fleshy leaves may form miniature bulbs (bulblets) that when grown to full size are known as offsets.
Green tea produced in the spring is made from the buds (apical or lateral), one leaf and one bud (one and a bud) or two leaves and one bud (two and a bud).
Its leaf, stem and bud are extremely compact in form of a round-shaped frond, resembling a single leaf.
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