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This review will first provide an overview of the gene microarray approach, including limitations and study design considerations.
There are several advantages to the oligonucleotide microarray approach, including uniformity of hybridization, probe performance and specificity, and the flexibility of customization or probe addition as more sequences enter the public domain [ 17- 20].
In addition to Bacillus spp., a few of the other species detected by our microarray approach including Pantoea spp., Acinetobacter spp., Pseudomonadaceae spp., and members of the Enterobacteriaceae family were recently detected in a study by Larsson et al. (2008) that investigated microbiological components of fresh tobacco leaves using culture methods.
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The benefits of this microarray approach include its high-throughput nature, reproducibility, small reaction surface along with even sera distribution across the surface, high dynamic range of signal intensities, and the quantity of data that one experiment can produce.
Hybridization-based microarray approaches, including array comparative genomic hybridization (array CGH) and Single Nucleotide Polymorphism (SNP) microarrays, have been used as an alternative technology to conventional cytogenetic approaches [ 39].
In this study we developed novel methods to determine the presence or divergence of all genes in a Staphylococcus aureus multistrain PCR product microarray-based CGH approach, including those that lack a reference signal by using performance data from all the spots on the microarray.
Samples were analyzed by applying a staged molecular approach, including multiplex MassTag PCR, 16S rRNA-gene PCR, DNA microarray, and high-throughput sequencing.
Examples of this approach include microarray based genome-wide expression analyses [15] and genotype detection for specific gene [16].
Our data integration approach includes microarray data normalization, transformation, and quality control.
For instance, promoter microarray-based approaches include the methylated CpG island amplification microarray chip (MCAM-chip) that utilizes enzymatic digestion [ 5, 6] and the methylated DNA immunoprecipitation microarray chip (MeDIP-chip) that employs antibody pulldown [ 12] to enrich methylated DNA.
Significant progress has been made in the identification of biomarkers by means of such technologies as DNA microarrays and proteomic approaches, including mass spectrometry, resulting in an increasing number of potential biomarker candidates.
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