Unknown,Transcriptomics,Genomics,Proteomics

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Rice ssRNA-seq


ABSTRACT: We took advantage of ssRNA-seq technology to deeply sequence mRNAs of the model plant species Oryza sativa ssp.japonica cv Nipponbare with clear transcriptional orientations for assessing rice cis-NATs at the best possible resolution. We also deeply sequenced rice small RNAs from the same tissues as that for preparing mRNAs to investigate rice cis-NAT pairs that potentially give rise to endogenous short interfering RNAs from their overlapping regions under normal and stress conditions.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Tingting Lu 

PROVIDER: E-MTAB-721 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.

Lu Tingting T   Zhu Chuanrang C   Lu Guojun G   Guo Yunli Y   Zhou Yan Y   Zhang Zhiyong Z   Zhao Yan Y   Li Wenjun W   Lu Ying Y   Tang Weihua W   Feng Qi Q   Han Bin B  

BMC genomics 20121222


<h4>Background</h4>Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRN  ...[more]

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