Transcriptomics,Genomics

Dataset Information

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Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (mRNA-seq)


ABSTRACT: Using Illumina’s high-throughput small RNA sequencing and RNA sequencing, miRNAs and mRNAs differentially expressed under Zn deficiency and Zn resupply conditions were identified in shoots and roots of rice seedlings. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply, and 38 of them were novel miRNAs. The Zn-responsive miRNAs were predicted to target a total of 799 genes. The transcriptome sequencing identified a total of 360 differentially expressed genes (DEGs) under Zn deficiency in shoots and roots, and 97 of them were recovered after Zn resupply treatment. Twelve DEGs were found to be potential targets genes of several Zn-responsive miRNAs like miR171g-5p, miR397b-5p, miR398a-5p, and miR528-5p. Overall design: Roots and shoots of rice seedlings were collected after Zn-deficient treatment for two weeks. For Zn-resupply treatment, Zn-deficient seedlings were transferred to nomal nutrient solution containing 1.5 µM ZnSO4 for three days. After Zn-resupply treatment, roots and shoots were collected for analyses at the same time point as collecting the Zn-deficient samples (four hours after illumination).

INSTRUMENT(S): Illumina HiSeq 4000 (Oryza sativa)

ORGANISM(S): Oryza sativa  

SUBMITTER: Houqing Zeng  

PROVIDER: GSE130980 | GEO | 2020-01-08

REPOSITORIES: GEO

Dataset's files

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Publications

Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings.

Zeng Houqing H   Zhang Xin X   Ding Ming M   Zhu Yiyong Y  

BMC plant biology 20191226 1


BACKGROUND:Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina's high-throughput small RNA sequencing and transcriptome sequen  ...[more]