Gene Expression
Nebulas
Gene Expression NebulasSummary: Stomata play a fundamental role modulating the exchange of gases between plants and the atmosphere. These microscopic structures form in high numbers on the leaf epidermis and are also present on flowers. Although leaf stomata are well-studied, little attention has been paid to the development or function of floral stomata. To characterise gene expression during the stomatal development in IR64 florets, as well as to identify potential gene expression differences in florets of transgenic plants with a reduction in stomatal density, a RNA-sequencing was carried out using floret samples from different developmental stages of IR64 (control) and transgenic plants overexpressing the gene OsEPF1. Differential expression analyses conducted on the RNA-seq dataset indicate that the cellular transitions during the development of floral stomata are regulated by the same genetic network used in rice leaves, and reveal alterations in global gene expression in florets of plants overexpressing OsEPF1.
Overall Design: This dataset includes samples of florets in the developing stages 1 to 5 and mature from IR64 (control) and OsEPF1-oe-S (transgenic) rice plants. Three biological replicates per sample type were sequenced.
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| Growth Protocol: | Plants were grown in Conviron growth cabinets under 12 h photoperiod (850 - 1000 µmol m-2 s-1 PAR at canopy level), 30°C day and 24°C night temperature, and 60 % relative humidity, with a constant supply of water to the pot base. From the 4th growth week, plants were fertilized in intervals of two weeks with Chempak High Nitrogen Feed No. 2 (Thompson & Morgan, Ipswich, UK). |
| Treatment Protocol: | - |
| Extract Protocol: | IR64 and OsEPF1-oeS developing florets were collected ~75-85 days after sowing, and mature florets were collected after panicle heading, but prior to anthesis (~ 95 days after sowing). RNA was extracted from floret samples using the Spectrum Plant Total RNA Kit (Sigma-Aldrich), with the On-Column DNase I Digest step, according to the manufacturer’s instructions. RNA samples extracted from developing florets of three individual plants were then mixed, in proportional RNA quantities. Therefore, each biological replicate for developing florets comprised RNA from three different rice plants. Three biological replicates per stage were sequenced. |
| Library Construction Protocol: | Enrichment of mRNA was carried out using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Biolabs), and library preparation was performed using the NEBNext Ultra RNA Library Prep Kit (Biolabs). |
| Molecule Type: | Poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NovaSeq 6133; Illumina NovaSeq 6134; Illumina NovaSeq 6135; Illumina NovaSeq 6136; Illumina NovaSeq 6137; Illumina NovaSeq 6138; Illumina NovaSeq 6139; Illumina NovaSeq 6140; Illumina NovaSeq 6141; Illumina NovaSeq 6142; Illumina NovaSeq 6143; Illumina NovaSeq 6144; Illumina NovaSeq 6145; Illumina NovaSeq 6146; Illumina NovaSeq 6147; Illumina NovaSeq 6148; Illumina NovaSeq 6149; Illumina NovaSeq 6150; Illumina NovaSeq 6151; Illumina NovaSeq 6152; Illumina NovaSeq 6153; Illumina NovaSeq 6154; Illumina NovaSeq 6155; Illumina NovaSeq 6156; Illumina NovaSeq 6157; Illumina NovaSeq 6158; Illumina NovaSeq 6159; Illumina NovaSeq 6160; Illumina NovaSeq 6161; Illumina NovaSeq 6162; Illumina NovaSeq 6163; Illumina NovaSeq 6164; Illumina NovaSeq 6165; Illumina NovaSeq 6166; Illumina NovaSeq 6167; Illumina NovaSeq 6168 |
| 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 | 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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