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We used technical replicates for control and TBM samples.
It has been observed that the GoldenSpike experiment uses technical replicates of a single experiment, rather than biological replicates.
Data variation between biological replicates with MPSS without technical replicates may understandably be larger than with microarrays when using sufficient numbers of replicates.
When we used four technical replicates, about 20% of genes expressed at relatively low levels (RPKM 3-30) did not reach their final RPKM, suggesting that these model settings were insufficient for calculating the real RPKM of genes expressed at low levels.
High Pearson correlation r values were found between technical replicates even when using different concentrations of RNA for amplification (Average 0.993; Range {0.977 to 0.997}).
For all experiments, statistical tests were performed with Microsoft Excel and GraphPad Prism software, using averaged technical replicates where possible.
The real-time PCR amplifications were performed using duplicate technical replicates.
The experiment was performed using two technical replicates for each independent biological replicate (n = 2).
The mean and standard error were determined using three technical replicates from one representative biological replicate.
Lysates of three biological replicates were analyzed with RPPA using four technical replicates of each.
When using such arrays, the number of required technical replicates is reduced because of the high degree of reproducibility between spots, allowing the user to concentrate resources on analyzing biological replicates.
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