Gene Expression
Nebulas
Gene Expression NebulasSummary: The rice gene SUB1A-1 confers flooding tolerance restricting shoot growth during submergence. Rice with SUB1A also show more rapid recovery after submergence ends, but mechanisms by which SUB1A improves recovery from submergence had not been examined. In this study, the transcriptome was sequenced at five time points over a 24 hour submergence recovery period in near-isogenic rice genotypes with and without SUB1A.
Overall Design: 36 samples, 2 genotypes: M202 and 202(Sub1), 2 conditions: unsubmerged and 3d whole shoot submergence, 5 time points: desubmergence (at midday following 3d submergence), dusk, midnight, dawn, midday (24 hours after desubmergence). 3 bioreplicates. Unsubmerged plants only sequenced for at desubmergence time point.
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| Growth Protocol: | Rice seeds (Oryza sativa L. ssp. japonica) of cultivar M202 and its near-isogenic, Sub1 introgression line, M202(Sub1), were sterilized for 30 min in a solution of 5% (v/v) bleach and 0.01% (v/v) Tween-20, rinsed and soaked overnight in DI water. After germinating in covered glass dishes on wet paper towels for 5 d, seedlings were transplanted into 10 cm pots in the greenhouse at a planting density of 20 plants per pot. Plants were grown in the greenhouse for 12 d before beginning the submergence treatment. |
| Treatment Protocol: | Plants were submerged in 121 L bins, in which water was allowed to equilibrate to ambient temperature for 24 h before submergence. Submergence began at ZT 6:00 and continued for 72 h, at which time plants were placed back on the greenhouse bench for reoxygenation. Whole shoots were harvested and flash-frozen in liquid N2 immediately upon desubmergence (3d_sub) at midday (ZT9:00), at dusk (ZT15:30), midnight (ZT19:45), dawn (ZT0), and again at midday 24 h following desubmergence (ZT9:00). |
| Extract Protocol: | Total RNA was isolated from frozen shoot tissue with the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). |
| Library Construction Protocol: | cDNA libraries for each sample were prepared from purified mRNA according to Wang et al. (2011). |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| 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 | 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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