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Branham, William S.; Melvin, Cathy D.; Han, Tao; Desai, Varsha G.; Moland, Carrie L.; Scully, Adam T; Fuscoe, James C.

doi:10.1186/1472-6750-7-8

Cited by 54 publications

(25 citation statements)

References 9 publications

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“…On the one hand, variation in signal intensity given by a certain oligonucleotide probe can occur among different experimental replicates and this might be related to differences in the quality of slides or solutions used for the hybridisation and washing steps. It is also reported that increased atmospheric ozone concentrations cause the oxidation of Cy5, hence decreasing fluorescence signal intensities [73], [74]. On the other hand, large differences in signal intensities among oligonucleotide probes might be related to the number and position of mismatches.…”

Section: Discussionmentioning

confidence: 99%

Identifying Fishes through DNA Barcodes and Microarrays

et al. 2010

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BackgroundInternational fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.Methodology/Principal FindingsThis study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.Conclusions/SignificanceBased on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

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Section: Discussionmentioning

confidence: 99%

Identifying Fishes through DNA Barcodes and Microarrays

et al. 2010

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“… 2 Since environmental ozone levels can have an effect on fluorescence intensity, ensure ozone levels are as low as 2 ppb prior to beginning hybridization unless the microarray laboratory has been installed with an adequate air filtering system (28, 29). A dye-flip experiment is performed to minimize any dye-effects.…”

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confidence: 99%

Comparison of Microarray and Quantitative Real-Time PCR Methods for Measuring MicroRNA Levels in MSC Cultures

Camarillo

Swerdel²,

Hart

2011

Methods in Molecular Biology

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The capacity for self-renewal and the multi-lineage potential of mesenchymal stromal cells (MSC) offers a therapeutic promise for regenerative medicine. MicroRNAs (miRNAs) are small non-coding RNAs that play a key regulatory role during differentiation both at the level of post-translational modulation and epigenetic control. Studies on MSCs have just begun to identify miRNA profiles in MSC and differentiated MSC. While several methods are available for miRNA exploration, microarrays and quantitative real-time PCR (qPCR) are the most common. Since there are several microarray and qPCR platforms available for miRNA detection, it is valuable to explore how these methods compare. We used the NCode Multi-Species miRNA microarray (Invitrogen) and the TaqMan Human microRNA array (Applied Biosystems) to compare microRNA expression in undifferentiated MSCs and MSCs differentiated into early osteoblasts. We show that while there is a somewhat low correlation between these two methods, there was a subset of miRNA measurements that did correlate.

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“…Note that all wash stock solutions should be filtered before using. After washing the Cy dyes are extremely unstable: Cy 5 is rapidly degraded by ozone in minutes (17, 18). Slides should be dried and scanned in a low ozone chamber; alternatively, some companies supply wash solutions that stabilize the dyes ( e.g.…”

Section: Transcription Profiling Methodsmentioning

confidence: 99%

Technical considerations in using DNA microarrays to define regulons

Rhodius

Wade

2009

Methods

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Transcription is the major regulatory target of gene expression in bacteria, and is controlled by many regulatory proteins and RNAs. Microarrays are a powerful tool to study the regulation of transcription on a genomic scale. Here we describe the use of transcription profiling and ChIP-chip to study transcriptional regulation in bacteria. Transcription profiling determines the outcome of regulatory events whereas ChIP-chip identifies the protein-DNA interactions that determine these events. Together they can provide detailed information on transcriptional regulatory systems.

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Cited by 54 publications

References 9 publications

Identifying Fishes through DNA Barcodes and Microarrays

Identifying Fishes through DNA Barcodes and Microarrays

Comparison of Microarray and Quantitative Real-Time PCR Methods for Measuring MicroRNA Levels in MSC Cultures

Technical considerations in using DNA microarrays to define regulons

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