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A different randomisation scheme was used for microarray sample processing to that used for tissue collection.
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Total RNA was isolated from islets samples according to the manufacturer's instructions following same protocols used for microarray RNA samples.
The study includes samples used for microarray hybridization and samples from independent treatments; a total of n = 8.
For each RNA extraction used for microarrays, a sample was collected in order to perform Q-PCR experiments.
In addition to the original samples used for microarray analysis, three new samples (two typhoid fever and one enterobacter) were obtained for Q-PCR validation.
Differential transcript levels for PAX1 and PAX5 were confirmed by quantitative RT-PCR in some of the RNA samples used for microarray analysis and RNA samples from an independent set (Figs. 8A and B).
To assess the quality of the RNA used for microarray experiments all samples were analysed using an Agilent Bioanalyser 2100.
Six NPs from the three histopathological groups for each breed type were analyzed (cDNA samples used for microarray and additional, similarly processed samples).
The characteristics of 10 selected genes are indicated in Table 2. RT-qPCR was performed on the samples used for microarray analysis as well as on samples generated from four additional independent experiments.
Quantitation of viral mRNAs in infected samples used for microarray allowed us to correlate host gene expression changes with relative infection levels.
Real-time RT-PCR was performed on the same RNA samples used for microarray analysis (TF1 shRPL5, TF1 shRPL11) or on different samples with a similar level of RP downregulation (TF1 shRPS19, both DOX-inducible model and transduced cells constitutively expressing shRNAs).
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