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As in the previous study, we prepared RNA from set2Δ and wild-type strains, and labeled them for direct comparison through microarray hybridization (Methods).
The microarray hybridization methods were as described in Pitre et al. (2010) [ 64].
However, throughput is greatly reduced, relative to endpoint analysis of agar spotted arrays, or the use of DNA microarray hybridization methods [ 4, 8, 17- 19].
Although hybridization-based methods, which allow screening RNA, DNA, or protein such as northern blot, southern blot, or western blot, respectively, are widely used, innovative and powerful microarray hybridization methods were developed in the 1990s.
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Superimposed upon this experimentally induced spot drop out are the differences inherent in the microarray hybridization method.
Recent studies using the microarray hybridization method suggest that cuticle-related genes may also be associated with resistance [ 21].
In an early study, a cross species microarray hybridization method was used for the detection of hypoxia induced expression patterns unique to Spalax[ 20].
The cDNA microarray hybridization method is now widely used to analyze simultaneously the expression of thousands of genes in cancer tissues [ 5, 21], but the contamination of tumors by epithelial, stromal or immune cells presents problems for obtaining accurate expression profiles.
The microarray platform, hybridization methods and data analysis have been described [ 10, 33].
For sample selection, cRNA preparation, microarray hybridization and normalization methods in this study see elsewhere [ 3].
In order to assess the reproducibility of microarray hybridization using standard methods, poly(A)+ RNA was isolated from both primary breast carcinoma BC2 and Universal Human Reference total RNA (Stratagene®).
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