RNA-seq

Polymorphisms in different EST-SSR types derived from the Chinese bayberry Myrica rubra, Myricaceae) transcriptome

S. Y. Zhang, Feng, C., Xu, C. J., Zhu, C. Q., and Chen, K. S., “Polymorphisms in different EST-SSR types derived from the Chinese bayberry Myrica rubra, Myricaceae) transcriptome”, vol. 14, pp. 6037-6041, 2015.

Most plant expressed sequence tag-simple sequence repeats (EST-SSRs) are not polymorphic, and it is important to learn the characteristics of highly polymorphic EST-SSRs. In this study, 357 compound and 5557 non-compound EST-SSRs, identified from the transcriptome of the Chinese bayberry (Myrica rubra ‘Biqi’), were divided into 11 types based on their characteristics. Polymorphisms in all 11 EST-SSR types were investigated in 10 cultivars.

RNA-seq reveals the downregulated proteins related to photosynthesis in growth-inhibited rice seedlings induced by low-energy N+ beam implantation

Q. F. Chen, Ya, H. Y., Wang, W. D., and Jiao, Z., “RNA-seq reveals the downregulated proteins related to photosynthesis in growth-inhibited rice seedlings induced by low-energy N+ beam implantation”, vol. 13, pp. 7029-7036, 2014.

Transcriptomic research based on RNA sequencing (RNA-seq) technology is innovative and will provide new opportunities and biological perspectives for the use of ion-beam implantation in plants. Using RNA-seq, transcriptomes of whole rice seedlings generated from seeds implanted with a low-energy N+ beam were analyzed 96 h after planting. We identified 544 transcripts that were differentially expressed genes (DEGs) in the non-growth-inhibited sample implanted by an N+ beam, including 262 upregulated transcripts and 282 downregulated transcripts.

Identifying differential expression genes and single nucleotide variations using RNA-seq in metastatic melanoma

D. Liu, Zhao, Z. G., Jiao, Z. L., and Li, H. J., “Identifying differential expression genes and single nucleotide variations using RNA-seq in metastatic melanoma”, vol. 13, pp. 8153-8162, 2014.

Melanoma is a malignant tumor and one of the most frequent metastatic cancers. This study was conducted to identify differential expression genes (DEGs) and single nucleotide variations (SNVs) in metastatic melanoma. We analyzed microarray data of GSE23056 downloaded from the Gene Expression Omnibus, including two normal samples (skinN1 and skinN2) and 2 metastatic melanoma samples (skinT and lymphT).

A generic plant RNA isolation method suitable for RNA-Seq and suppression subtractive hybridization

Y. Q. Zhu, Wu, W. J., Xiao, H. W., Chen, H. B., Zheng, Y., Zhang, Y. J., .X.Wang, H., and Huang, L. Q., “A generic plant RNA isolation method suitable for RNA-Seq and suppression subtractive hybridization”, vol. 12, pp. 5537-5546, 2013.

A recently developed revolutionary approach to transcrip­tomics, RNA-Seq, and suppression subtractive hybridization are power­ful tools for gene expression research. However, currently, the difficulty of isolating high-quality RNAs from plant tissues bearing abundant complex polysaccharides, polyphenolics, and secondary metabolites is a serious problem that not only limits the application of these technologies but also hinders studies dealing with RNA in general.

Application of RNA-seq to reveal the transcript profile in bacteria

A. C. Pinto, Melo-Barbosa, H. P., Miyoshi, A., Silva, A., and Azevedo, V., “Application of RNA-seq to reveal the transcript profile in bacteria”, vol. 10. pp. 1707-1718, 2011.

The large number of microbial genomes deposited in databanks has opened the door for in-depth studies of organisms, including post-genomics investigations. Thanks to new generation sequencing technology, these studies have made advances that have lead to extraordinary discoveries in bacterial transcriptomics. In this review, we describe bacterial RNA sequencing studies that use these new techniques.

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