Gene Expression
Nebulas
Gene Expression NebulasSummary: The mRNA expression profiles of the hypocotyl and root in WT and hy5 were analyzed in 24 hour 22degC and 28degC treated condition. The gene expression changes were analyzed and compared within 22degC and 28degC and in different tissue type (hypocotyl vs root).
Overall Design: Total twentiefour 24h 22degC and 28degC treated Arabidopsis samples were used. These include three replicates of following genotypes; Col-0 and hy5, with two tissue type; hypocotyl and root. Therefore, three replicates of following genotypes, tissue and conditions; Col-0 (hypocotyl-22degC), Col-0 (root-22degC), hy5 (hypocotyl-22degC), hy5 (root-22degC), Col-0 (hypocotyl-28degC), Col-0 (root-28degC), hy5 (hypocotyl-28degC), hy5 (root-28degC).
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| Growth Protocol: | Total three genotypes; Col-0, hec1hec2 and pifQ plants were used for mRNA sequencing analysis. |
| Treatment Protocol: | The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days in dark to induce germination. After three days, seeds were further treated 5 days in 22℃ with white light (25 µmole/s2/m2). After 5 days, seedlings were either treated with 4 hour of continuous white light (25 µmole/s2/m2) in 22 or 28. |
| Extract Protocol: | Total RNA was isolated using sigma plant total RNA kit(Sigma, Cat.# STRN250). |
| Library Construction Protocol: | 3'Tag-Seq method article was used to generate TagSeq library according to the manufacturer’s instruction. (doi: 10.1111/1755-0998.12529) |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | SINGLE |
| Library Strand: | Reverse |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NovaSeq 6000 |
| 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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