Gene Expression
Nebulas
Gene Expression NebulasSummary: Two types of small (18-24 nt) non-coding RNAs (ncRNAs), microRNAs (miRNAs) and small interfering RNAs (siRNAs) have been found to exist widely in higher plants. OsDCL3b has just been reported to process the 24-nt phased small RNAs in rice, which are preferentially expressed in panicle. In this study, we find that down-regulated expression of OsDCL3b leads to lower pollen sterility and seed setting rate, which results in decreased grain yield per plant in rice. Next, small RNA and mRNA sequencing were performed to study the decrease of pollen fertility and seed setting rate. 942 differentially expressed genes were identified, and some of them have already been known to be involved in rice panicle development. Our results indicate that there is a close correlation between small RNA and rice yield.
Overall Design: RNA-seq and small RNA-seq from wild-type and dcl3b knockdown mutant rice.
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| Growth Protocol: | Rice plants were grown in the paddy field. |
| Treatment Protocol: | - |
| Extract Protocol: | Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (Ambion) for removing DNA contamination. |
| Library Construction Protocol: | Libraries were constructed through applying TruSeq Small RNA sample preparation and TruSeq Stranded mRNA kits (Illumina, San Diego, CA, USA) for small RNA sequencing and RNA sequencing, respectively, in accordance with the manufacturer’s instruction. |
| Molecule Type: | rRNA- 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 | 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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