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If we replicate Figure 4 times, the total expected energy consumption becomes (30).
With the number of singletons (single sequence-containing OTUs) ranging from 12 to 33 for each sample A replicate library, the variation observed for the OTU analysis was expected, as was that observed between the separate sequencing runs for the single (Figure 4) versus replicate (Figure 5) sample A analyses (i.e. gram-positive Firmicutes remained dominant at 50-60% and 70-75%, respectively).
In the symetrical experiment, with 104 amoebae, plaques were observed for a single replicate (Figure 1 (D)).
In contrast to unique sequences, 67% of hotspots were represented in more than one replicate (Figure 1).
However, at 4-BPB concentrations greater than 0.5 µM invaded parasites were inhibited in replication and remained permanently in single-parasite vacuoles even when they were given 48 hrs to invade and replicate (Figure 1C) and failed to lyse out of their host cell after 2 weeks (data not shown).
Their suggested methodology can only replicate Figure 2 in my article, which shows the cumulative distribution of the mean frequencies of individual incubation periods.
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At this stage, one must carefully select the sample material (e.g., cells, tissues, organism), conditions for cultivation, and the strategy for harvesting, ensuring a minimal number of replicates (Figure 1A).
Our experimental design of using stress and control with multiple sampling during a time-course of chilling stress and subsequent recovery was demonstrated to be powerful to quantify the chilling induced dynamic changes of the major groups of primary metabolites in rice, evidenced by the consistent PCA results of the three biological replicates (Figure 2, Additional file 2: Table S2).
Pico Profiling showed much higher correlation of replicates (Figure 5A) than replicates of Kurimoto's data set (Figure 5C), and also outperformed Jensen's expression profiles for correlation between replicates (Figure 5B).
We analyzed expression levels between replicates and found a high congruency among replicates (Figure 10A and B).
We found only ∼1.4% of unique sequences were shared among all three replicates, and only ∼5.9% between at least two replicates (Figure 1a).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com