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

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

PROVIDER: PRJNA542271 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9040300.fastq.gz	Fastqsanger.gz
	SRR9040310.fastq.gz	Fastqsanger.gz
	SRR9040301.fastq.gz	Fastqsanger.gz
	SRR9040311.fastq.gz	Fastqsanger.gz
	SRR9040302.fastq.gz	Fastqsanger.gz

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

Project description:Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery

| PRJNA542268 | ENA

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

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

| PRJNA542164 | ENA

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

Project description: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.

2020-01-08 | GSE130980 | GEO

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

2020-01-08 | GSE131003 | GEO

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

Project description: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 sequencing. RESULTS:The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results. CONCLUSION:These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.

| S-EPMC6933703 | biostudies-literature

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-01-08 | GSE131004 | GEO

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under salt stress and recovery stage

Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from salt stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.

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Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under cold stress and recovery stage

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Integrated multi-omics analysis of zinc deficiency

Project description:Zinc is an essential trace micronutrient and exerts important physiological and biochemical roles. Zinc deficiency is a global public-health problem. Standing untreated zinc deficiency can cause series adverse effects, including growth retardation, poor appetite, delayed sexual development, impaired neurologic and immune systems, diabetes and obesity, et al. However, the underlying mechanisms of these adverse effects remain elusive in most cases and a comprehensive understanding of the adverse effects (known and unknown) induced by zinc deficiency is lacking. As we know, zinc is a critical component of over 3000 enzymes and is required for numerous catalytic, structural, and regulatory functions of proteins. Thus, the impairments in enzyme actions are responsible for the gross symptoms of zinc deficiency. Altered enzymes may induce to the extensive changes in diverse molecular components of body, including DNA, mRNA and metabolites; and all above changes may work together to induce the adverse effects and affect the health of body. Therefore, protein changes associated with zinc deficiency are very necessary to be unraveled and described for revealing the known and unknown adverse effects and underlying mechanisms. In this project, we first performed a multi-omics study by integrating plasma metabolomics and proteomics, liver proteomics and metal ionomics on zinc deficient rats in order to identify biomarkers (proteins, metabolites and metal elements) of zinc deficiency and reveal the changed metabolic pathways. Eventually, we expected to completely present known adverse effects and their underlying molecular mechanisms, and uncover unknown adverse effects of zinc deficiency.

2019-06-05 | PXD014079 |

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Project description:Interaction Mechanism of Soybean Seedlings with Engineered and Bio-synthesized Zinc Nanoparticles on Proteomics Perspective

2023-04-13 | PXD017688 | JPOST Repository