Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana

ABSTRACT: We sequenced the total RNA from a tissues mixed sample (inflorescences, rosette leaves, cauline leaves and stems) of Arabidopsis thaliana. After total RNA extraction, the same amount of tissue RNA were mixed. Ribosomal RNAs were deleted from the mixed tissue total RNAs using RiboMinus™ Plant Kit repeated three times. We also sequenced 9 poly(A)- RNAs from seedlings treated with different stress conditions at different times. The poly(A)- RNAs were collected by removing poly(A)+ RNAs four times . Then rRNAs were removed from poly(A)- RNAs three times. Sequencing of total RNAs from the mixed tissues sample is taken as an example of collecting novel transcripts from high-throughput data, which could be clarified by noncoding scores derived from our integrative models. Sequencing of nonpolyA RNAs are used for identifing stress-responsive nonpolyA lncRNAs and for validation of predicted lncRNAs.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Zhi Lu

PROVIDER: E-GEOD-49325 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.

Di Chao C Yuan Jiapei J Wu Yue Y Li Jingrui J Lin Huixin H Hu Long L Zhang Ting T Qi Yijun Y Gerstein Mark B MB Guo Yan Y Lu Zhi John ZJ

The Plant journal : for cell and molecular biology 20141021 5

Recently, in addition to poly(A)+ long non-coding RNAs (lncRNAs), many lncRNAs without poly(A) tails, have been characterized in mammals. However, the non-polyA lncRNAs and their conserved motifs, especially those associated with environmental stresses, have not been fully investigated in plant genomes. We performed poly(A)- RNA-seq for seedlings of Arabidopsis thaliana under four stress conditions, and predicted lncRNA transcripts. We classified the lncRNAs into three confidence levels accordin ...[more]

PMID: 25256571

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Dataset Information

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana

Publications

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.

Similar Datasets

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