Gene Expression
Nebulas
Gene Expression NebulasSummary: This study evaluated transcriptomic responses to submergence in elongating and non-elongating leaves of rice near-isogenic lines with and without SUB1A using RNA-Seq. SUB1A is an ERF transcription factor gene and the key regulator of submergence tolerance in rice, restricting underwater elongation and avoiding starvation under the stress. Submergence induces mRNA accumulation of SUB1A similarly in elongating and non-elongating leaves. This study uncovered SUB1A-dependent and independent regulation of adaptive responses to submergence in the two functionally distinct leaves at the global level.
Overall Design: mRNAs extracted from elongating and non-elongating leaves of rice plants [M202 and M202(Sub1)] submerged for 0, 1, 3, and 6 days. Three independent biological replicates.
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| Growth Protocol: | Rice plants were grown in pots in a greenhouse until the 4.2-leaf stage. |
| Treatment Protocol: | Plants were completely submerged for 0, 1, 3, and 6 days. Immediately after de-submergence at each time point, the 5th (elongating) leaves and lower (non-elongating) leaves were separated, frozen in liquid nitrogen, and stored at -80C until use. |
| Extract Protocol: | Total RNAs were extracted from frozen tissues using a miRNeasy Mini kit (Qiagen, Hilden, Germany). Genomic DNA was eliminated by on-column digestion. |
| Library Construction Protocol: | RNA-Seq libraries were prepared for sequencing using standard Illumina protocols |
| Molecule Type: | Poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Reverse |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NovaSeq 6085; Illumina NovaSeq 6086; Illumina NovaSeq 6087; Illumina NovaSeq 6088; Illumina NovaSeq 6089; Illumina NovaSeq 6090; Illumina NovaSeq 6091; Illumina NovaSeq 6092; Illumina NovaSeq 6093; Illumina NovaSeq 6094; Illumina NovaSeq 6095; Illumina NovaSeq 6096; Illumina NovaSeq 6097; Illumina NovaSeq 6098; Illumina NovaSeq 6099; Illumina NovaSeq 6100; Illumina NovaSeq 6101; Illumina NovaSeq 6102; Illumina NovaSeq 6103; Illumina NovaSeq 6104; Illumina NovaSeq 6105; Illumina NovaSeq 6106; Illumina NovaSeq 6107; Illumina NovaSeq 6108; Illumina NovaSeq 6109; Illumina NovaSeq 6110; Illumina NovaSeq 6111; Illumina NovaSeq 6112; Illumina NovaSeq 6113; Illumina NovaSeq 6114; Illumina NovaSeq 6115; Illumina NovaSeq 6116; Illumina NovaSeq 6117; Illumina NovaSeq 6118; Illumina NovaSeq 6119; Illumina NovaSeq 6120; Illumina NovaSeq 6121; Illumina NovaSeq 6122; Illumina NovaSeq 6123; Illumina NovaSeq 6124; Illumina NovaSeq 6125; Illumina NovaSeq 6126; Illumina NovaSeq 6127; Illumina NovaSeq 6128; Illumina NovaSeq 6129; Illumina NovaSeq 6130; Illumina NovaSeq 6131; Illumina NovaSeq 6132 |
| Strand-Specific: | Specific |
| 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 | Condition 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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