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For example, the traditional whole-genome array for expression studies in Arabidopsis thaliana usually contains only 23k oligos, while a customized whole-genome tiling array tiled at ∼250 bp resolution may contain ∼400k oligos.
To identify putatively tissue-specific genes and demonstrate the utility of this array for expression profiling in a variety of peanut tissues, we compared transcript levels in pod, peg, leaf, stem, and root tissues.
To test the utility of this array for expression studies in both vegetative and reproductive tissues and identify putatively pod-specific genes, we compared transcript abundance in pod, leaf, stem, root, and peg tissues.
In order to elucidate the interactive networks and to identify novel Arabidopsis mutants impaired in chloroplast gene expression, we have established macroarrays and complemented our results with data acquired using the Affymetrix 22K arrayarray for expression profiling.
We have developed a high-density oligonucleotide microarray for peanut using 49,205 publicly available ESTs and tested the utility of this array for expression profiling in a variety of peanut tissues.
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All sequences were de novo assembled and the final annotated sequences were used to construct a customized oligo-array for expression profiling of the GSB intestine using a factorial design (2x2) with diet composition and parasite infection as experimental variables.
The Agilent Gene Expression Array Platform provides an extremely flexible custom array format for creating arrays for expression analysis.
The situation became more complex as investigators began using long oligonucleotide arrays for expression profiling [ 5- 9].
We used two separate NimbleGen high-density arrays for expression analysis (design name = HG18 60 mer expr 4plex and design name = MM8 60 mer expr X4).
One such in vitro application would be the creation of virus arrays for expression and functional analysis of genes [ 13, 14].
To obtain the 3,700 arrays for expression profiling, an initial batch of 5,700 CEL files was downloaded from Gene Expression Omnibus, and each file was evaluated according to four quality control criteria (average background, scale factor, percent present, RNA degradation) [ 101].
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