Detection of transcriptional difference of porcine imprinted genes using different microarray platforms

Tsai, Shengdar Q.; Mir, Bashir Ahmed; Martin, Amy C; Estrada, José L.; Bischoff, Steve; Hsieh, Wu‐Chiao; Cassady, J. P.; Freking, B. A.; Nonneman, Dan; Rohrer, G. A.; Piedrahita, Jorge A.

doi:10.1186/1471-2164-7-328

Cited by 28 publications

(24 citation statements)

References 24 publications

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“…In order to find as many genes as possible that may be function in the trait, our study related global gene expression profiles to muscle fatty acid composition. Affymetrix Porcine Genome Array was applied according to its sensitivity and reproducibility for swine genomic studies 22. Although fold changes of the selected genes were not exactly same between real-time PCR assay and microarray assay, the expression tendencies were highly consistent, suggesting that the data from microarray assay in our study was reliable.…”

Section: Discussionmentioning

confidence: 79%

Fatty Acid and Transcriptome Profiling of Longissimus Dorsi Muscles between Pig Breeds Differing in Meat Quality

Shu²,

Yuan³

et al. 2013

Int. J. Biol. Sci.

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Fat and lean pig breeds show obvious differences in meat quality characteristics including the fatty acid composition of muscle. However, the molecular mechanism underlying these phenotypes differences remains unknown. This study compared meat quality traits between Lantang (a Chinese indigenous breed) and Landrace (a typical lean breed). The Lantang pigs showed higher L* values and intramuscular fat content, lower pH45min, pH24h and shear force in longissimus dorsi (LD) muscle than Landrace (P < 0.05). Fatty acid analysis demonstrated the lower monounsaturated fatty acids (MUFA) and higher polyunsaturated fatty acids (PUFA) percentage in Lantang LD than that in Landrace LD (P < 0.05). To further identify candidate genes for fatty acid composition, the transcriptome of LD muscle from the two breeds were measured by microarrays. There were 586 transcripts differentially expressed, of which 267 transcripts were highly expressed in Lantang pigs. After the validation by real-time quantitative PCR, 13 genes were determined as candidate genes for fatty acid composition of muscle, including Stearoyl-CoA desaturase (SCD). Then, a SCD over-expression plasmid was transfected into C2C12 cells to reveal the effect of SCD on the fatty acid composition in vitro. The results showed that SCD over-expression significantly increased PUFA proportion, while reduced that of saturated fatty acids (SFA) in C2C12 cells (P < 0.05). In summary, this study compared the differences of fatty acid composition and transcriptome in two breeds differing in meat quality, and further identified the novel role of SCD in the regulation of PUFA deposition.

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Section: Discussionmentioning

confidence: 79%

Fatty Acid and Transcriptome Profiling of Longissimus Dorsi Muscles between Pig Breeds Differing in Meat Quality

Shu²,

Yuan³

et al. 2013

Int. J. Biol. Sci.

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“…Long oligonucleotide arrays are also considered to be an improvement over cDNA arrays as they eradicate the problem of clone misidentification and erroneous cross hybridisation [13]. The use of the long oligonucleotide whole genome chicken array as a tool in comparative genomics for other avian species has been validated in this study.…”

Section: Discussionmentioning

confidence: 99%

Application of chicken microarrays for gene expression analysis in other avian species

et al. 2009

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BackgroundWith the threat of emerging infectious diseases such as avian influenza, whose natural hosts are thought to be a variety of wild water birds including duck, we are armed with very few genomic resources to investigate large scale immunological gene expression studies in avian species. Multiple options exist for conducting large gene expression studies in chickens and in this study we explore the feasibility of using one of these tools to investigate gene expression in other avian species.ResultsIn this study we utilised a whole genome long oligonucleotide chicken microarray to assess the utility of cross species hybridisation (CSH). We successfully hybridised a number of different avian species to this array, obtaining reliable signals. We were able to distinguish ducks that were infected with avian influenza from uninfected ducks using this microarray platform. In addition, we were able to detect known chicken immunological genes in all of the hybridised avian species.ConclusionCross species hybridisation using long oligonucleotide microarrays is a powerful tool to study the immune response in avian species with little available genomic information. The present study validated the use of the whole genome long oligonucleotide chicken microarray to investigate gene expression in a range of avian species.

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“…It is well documented that probe specificity and sensitivity depend on multiple factors including uniqueness, GC content, steric hindrance, optimal melting temperature and distance from the 3′ end of the ORF (Tsai et al 2006; Hughes et al 2001; Nakaya et al 2007). …”

Section: Methodsmentioning

confidence: 99%

Identification of sense and antisense transcripts regulated by drought in sugarcane

et al. 2012

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Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90 %. From the probes presented on the array, 75 % of the sense probes and 11.9 % of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-012-9922-1) contains supplementary material, which is available to authorized users.

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Detection of transcriptional difference of porcine imprinted genes using different microarray platforms

Cited by 28 publications

References 24 publications

Fatty Acid and Transcriptome Profiling of Longissimus Dorsi Muscles between Pig Breeds Differing in Meat Quality

Fatty Acid and Transcriptome Profiling of Longissimus Dorsi Muscles between Pig Breeds Differing in Meat Quality

Application of chicken microarrays for gene expression analysis in other avian species

Identification of sense and antisense transcripts regulated by drought in sugarcane

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