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Biological replicates were then assigned a single median value for each gene and time point.
Means of three biological replicates were then plotted using Microsoft Excel.
For each treatment, total RNAs from the 3 biological replicates were then pooled together in equal proportions.
For each strain, experimental values from three biological replicates were then compared to those calculated from three computational simulations with matching starting biomass values under aerobic and anaerobic conditions.
Mixture samples collected from every 20 rows of the MES-treated or mock-treated plants were used as one biological replicate, and three independent biological replicates were then prepared for each sample.
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The reproducibility across biological replicates is then investigated as an internal validation of the detections.
For each strain, total RNA from the three biological replicates was then pooled together in equal proportions.
Reproducibility between iCLIP biological replicates was then analyzed, and clusters with greater than or equal to five cDNA counts reproduced in at least two independent iCLIP experiments were selected (Table S3).
That is, all data from all experimental replicates of both cybrid strains with AF16 nuclear and HK104 mitochondrial genotypes (CP129 and CP130, the biological replicates) were combined and then compared to AF16; all CP131 and CP133 cybrid data (HK104 nuclear and AF16 mitochondrial genotypes) were combined and then compared to HK104.
The biological replicates were advantageous because DESeq is then able to determine a much better variance estimate for each transcript improving the statistical power of the experiment.
This matrix was then used on all 34 bacilli and each bacteria was grown 5 times and each of these biological replicates were analysed 4 times (technical replicates).
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