Gene Expression
Nebulas
Gene Expression NebulasSummary: Arsenic (As) is a carcinogenic metalloid that is a contaminant widely polluting rice paddy soils around the world. In order to gain better insight into molecular mechanism of rice exposed to As(III) stress, we used next-generation sequencing technology to acquire global transcriptome alteration and miRNA regulation in rice upon As(III) treatments. Our results suggest time course and As(III)-dosing treatments were devised. Cluster analyses show that root and shoot samples were differentially grouped. For roots, sub-clusters were more distinct in the dosage course whereas for shoots they were most recognizable for the time course treatments. Other than the significantly regulated gene expression in the heavy metal-responsive sulfur and glutathione metabolism pathways, the expression of genes related to heavy metal transportation, jasmonate biosynthesis and signaling pathways, lipid metabolism and gene transcription were sharply regulated, indicating that rice allocates energy and resources from growth to stress response under As(III) stress. In addition to the detection of previously identified stress-related miRNAs, we further discovered 36 new As(III)-responsive miRNAs. These results expand our understanding of As(III) stress mechanism to the As(III)-responsive mRNA and miRNA transcriptomes, which provide a foundation for subsequent functional research.
Overall Design: 10 mRNA samples examined
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| Growth Protocol: | Seedlings were grown in 1/2 Hoagland nutrient solution at 28°C day/ 25°C night with a photoperiod of 16 h light (9:00-0:59) and 8 h night (1:00-8:59) in the green house. |
| Treatment Protocol: | For As(III) treatments, 14-d-old rice seedlings were exposed to sodium arsenite (20 and 80 μm) at 9:00, and materials were harvested at 0, 6 and 24 h after treatment. |
| Extract Protocol: | Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions and was treated with RNase-free DNase I (New England Biolabs) to remove contaminated genomic DNA. mRNA was isolated from total RNA using Dynabeads oligo(dT) (Invitrogen). First- and second-strand cDNA were generated using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. |
| Library Construction Protocol: | Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction according to the illuminaIllumina paired-end sample preparation protocol, using custom multiplex indexed Solexa adaptors and sequenced as 75 × 2 using the Illumina GA Genome Analyzer paired-end pipeline. |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina Genome Analyzer IIx |
| Strand-Specific: | Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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