Gene Expression
Nebulas
Gene Expression NebulasSummary: Environmental conditions, such as photoperiod and temperature, can affect male fertility in plants. While this feature is heavily exploited in rice to generate male-sterile lines for hybrid breeding, the underlying molecular mechanisms remain largely unknown. In this study, we use a transcriptomics approach to identify key genes and regulatory networks affecting pollen maturation in rice anthers in response to different day lengths.This work provides a new understanding on photoperiodsensitive pollen development in rice, and our gene expression database will provide a new, comprehensive resource to identify new environmentally sensitive genes regulating male fertility for use in crop improvement.
Overall Design: the mitosis stages I anther were collected at 08:00,12:00,16:00,20:00,00:00, 04:00 in sort-day(12 hours light) and long-day(14 hours dark) condition., each sample have two biological replicates.
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| Growth Protocol: | Rice variety Oryza sativa L. ssp. japonica 9522 was grown in paddy fields around Shanghai (China) during the normal rice growing season (June–August). |
| Treatment Protocol: | Photoperiod treatment was started after panicle initiation and continued until all samples were collected: LD was the natural daylight condition, with a photoperiod of ~14 h; SD conditions were simulated by covering plants with black cloth for the last 2 h of natural daylight to create a 12 h photoperiod. |
| Extract Protocol: | RNA was harvested using Trizol reagent (Invitrogen). |
| Library Construction Protocol: | RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol |
| Molecule Type: | rRNA- RNA |
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| Library Layout: | SINGLE |
| Library Strand: | Reverse |
| Platform: | ION_TORRENT |
| Instrument Model: | Ion Torrent Proton |
| 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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