Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

Hammond, John P.; Broadley, Martin R.; Craigon, David J.; Higgins, Janet; Emmerson, Z. F.; Townsend, Henrik J; White, Philip J.; May, Sean

doi:10.1186/1746-4811-1-10

Cited by 74 publications

(64 citation statements)

References 23 publications

(34 reference statements)

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“…The number of probe-pairs retained for analysis decreased rapidly (Additional file 1) as the DNA hybridization threshold was increased. In comparison the number of probe-sets reduced at a slower rate, which was consistent with the results obtained with other species [11,12]. The number of differentially expressed genes (fold change >1.25, p<0.05) was calculated at each threshold and the mask value of 75 returned the highest number of differentially expressed putative genes (414 probe-sets) (Additional file 2).…”

Section: Resultssupporting

confidence: 84%

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Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

et al. 2012

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BackgroundPapaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during papaya fruit ripening and their control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana.ResultsPapaya transcriptome analyses resulted in the identification of 414 ripening-related genes with some having their expression validated by qPCR. The transcription profile was compared with that from ripening tomato and grape. There were many similarities between papaya and tomato especially with respect to the expression of genes encoding proteins involved in primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicated that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families were involved in the control of papaya ripening and revealed that cell wall-related gene expression in papaya had similarities to the expression profiles seen in Arabidopsis during hypocotyl development.ConclusionThe cross-species array experiment identified a ripening-related set of genes in papaya allowing the comparison of transcription control between papaya and other fruit bearing taxa during the ripening process.

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Section: Resultssupporting

confidence: 84%

“…Commercial oligo-chips are not currently available for these organisms and comprehensive RNA sequencing can still be costly often prohibiting routine experiments. However, a cross-species (XSpecies) microarray is an alternative approach that has been successfully used to study the transcriptomes of non-model organisms [11,12]. …”

Section: Introductionmentioning

confidence: 99%

Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

et al. 2012

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“…The RQ values for each experiment were averaged to provide the mean change in gene expression compared to controls. Changes in gene expression greater than 30% of the control values were considered biologically relevant as previously described (Johnson et al 2007; Hammond et al 2005). Genes were grouped according to their classifications (e.g., osteoblast, SMC, EC) to help detect trends in related end points.…”

Section: Methodsmentioning

confidence: 99%

Mechanical stimuli differentially control stem cell behavior: morphology, proliferation, and differentiation

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Nieponice

et al. 2011

Biomech Model Mechanobiol

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Mesenchymal stem cell (MSC) therapy has demonstrated applications in vascular regenerative medicine. Although blood vessels exist in a mechanically dynamic environment, there has been no rigorous, systematic analysis of mechanical stimulation on stem cell differentiation. We hypothesize that mechanical stimuli, relevant to the vasculature, can differentiate MSCs toward smooth muscle (SMCs) and endothelial cells (ECs). This was tested using a unique experimental platform to differentially apply various mechanical stimuli in parallel. Three forces, cyclic stretch, cyclic pressure, and laminar shear stress, were applied independently to mimic several vascular physiologic conditions. Experiments were conducted using subconfluent MSCs for 5 days and demonstrated significant effects on morphology and proliferation depending upon the type, magnitude, frequency, and duration of applied stimulation. We have defined thresholds of cyclic stretch that potentiate SMC protein expression, but did not find EC protein expression under any condition tested. However, a second set of experiments performed at confluence and aimed to elicit the temporal gene expression response of a select magnitude of each stimulus revealed that EC gene expression can be increased with cyclic pressure and shear stress in a cell-contact-dependent manner. Further, these MSCs also appear to express genes from multiple lineages simultaneously which may warrant further investigation into post-transcriptional mechanisms for controlling protein expression. To our knowledge, this is the first systematic examination of the effects of mechanical stimulation on MSCs and has implications for the understanding of stem cell biology, as well as potential bioreactor designs for tissue engineering and cell therapy applications.

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“…This was first demonstrated by Ranz et al [17] for two closely related species of Drosophila , and has been successfully applied in land plants [18,19]. The results from such CGH experiments can be used to mask probes with high inter-strain and inter-species variability, thus increasing the accuracy of expression analyses carried out with alternative strains or species.…”

Section: Introductionmentioning

confidence: 99%

Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

et al. 2011

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BackgroundBrown algae of the genus Ectocarpus exhibit high levels of genetic diversity and variability in morphological and physiological characteristics. With the establishment of E. siliculosus as a model and the availability of a complete genome sequence, it is now of interest to analyze variability among different species, ecotypes, and strains of the genus Ectocarpus both at the genome and the transcriptome level.ResultsWe used an E. siliculosus gene expression microarray based on EST sequences from the genome-sequenced strain (reference strain) to carry out comparative genome hybridizations for five Ectocarpus strains: four E. siliculosus isolates (the male genome strain, a female strain used for outcrosses with the genome strain, a strain isolated from freshwater, and a highly copper-tolerant strain), as well as one strain of the sister species E. fasciculatus. Our results revealed significant genomic differences between ecotypes of the same species, and enable the selection of conserved probes for future microarray experiments with these strains. In the two closely related strains (a male and a female strain used for crosses), genomic differences were also detected, but concentrated in two smaller genomic regions, one of which corresponds to a viral insertion site.ConclusionThe high variability between strains supports the concept of E. siliculosus as a complex of cryptic species. Moreover, our data suggest that several parts of the Ectocarpus genome may have evolved at different rates: high variability was detected particularly in transposable elements and fucoxanthin chlorophyll a/c binding proteins.

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Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

Cited by 74 publications

References 23 publications

Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

Mechanical stimuli differentially control stem cell behavior: morphology, proliferation, and differentiation

Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

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