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We present here the design principles of the modENCODE DCC, and describe the ramifications of collecting thorough and deep metadata for describing experiments, including the use of a wiki for capturing protocol and reagent information, and the BIR-TAB specification for linking biological samples to experimental results.
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Thirdly, conventional triaxial shearing tests have been conducted for 34 sets of soil samples to provide experimental data for training and validating the neural network model.
Previous experiments [ 2- 4] only required 49 samples to show experimental indistinguishability, in part because prolonged rather than bolus dosing was used.
Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation).
Taken together, our study and that of Kang and Marjoram (2012) demonstrate the value of sensible use of genealogical relationships among samples to improve experimental design for sequencing studies.
We quantified the effects of our algal treatments on the concentration of DOC by collecting water samples proximate to experimental corals and algal pouches in experiments 1 and 2 (n = 5/treatment/experiment).
We found that QLT followed by QPN [80] improved the correct clustering of samples according to experimental groups (MNs, dCINs and MIX) compared with either normalization procedure used alone.
The batch effects problem is a non-biological systematic bias that exists in various batches of samples due to experimental handling.
We performed FDTD simulations on these samples to verify the experimental observations.
The sample labelling and fractionation were performed twice using the same pool of samples to generate an experimental replicate.
Then the data were median-centered and normalized for each sample, to remove experimental biases.
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