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Genome Information for Solanum lycopersicum
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Purpose: To identify genes regulated by SlDOF1 during fruit ripening, we performed RNAseq experiments with three biological replicates and compared the transcriptom profiles of SlDOF1-RNAi and wild-type fruit at breaker stage.
Methods: Expression profiles of wild-type (wt) and SlDof1-RNAi fruits (SlDof-8-RNAi) at 38 days after poliation (dpa) were generated by deep sequencing with three replicates using Illumina HiSeqTM 2000. RNA-seq reads obtained from the replicate were further filtered and aligned against the whole tomato genome. Differential expressed genes between samples were defined by DESeq software using two separate models, based on PPEE > 0.05 and false discovery rate (FDR)<0.001. Quantitative RT–PCR was performed using SYBR Green assays.
Results: A total of 1728 differentially expressed genes were identified in the SlDof1 RNAi fruit compared with the wild type and among them were a number of ripening-relate genes.
Overall design: Expression profiles of wt and SlDof1-RNAi fruits at 38 dpa were generated by RNA deep sequencing, with three replicates, using Illumina HiSeqTM 2000
| Accession | PRJNA489385; GEO: GSE119493 |
| Data Type | Transcriptome or Gene expression |
| Scope | Multiisolate |
| Organism | Solanum lycopersicum[Taxonomy ID: 4081] Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Solanum subgen. Lycopersicon; Solanum lycopersicum |
| Submission | Registration date: 5-Sep-2018
Institute of botany, the chinese academy of sciences |
| Relevance | Agricultural |
Project Data:
| Resource Name | Number
of Links |
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| Sequence data |
| SRA Experiments | 6 |
| Other datasets |
| BioSample | 6 |
| GEO DataSets | 1 |