Datasets
| Name | Description | Type |
|---|---|---|
| Whole Genome Assembly and Annotation of MH63 |
The Rice Information GateWay (RIGW) was upgraded to Version 3.0 with the release of GAP-FREE reference genome assemblies of MH63. |
Annotation of a genome. |
| Whole Genome Assembly and Annotation of ZS97 |
The Rice Information GateWay (RIGW) was upgraded to Version 3.0 with the release of GAP-FREE reference genome assemblies, ZS97RS3. |
Annotation of a genome. |
| Transcriptional rice responses to PGPR Burkholderia |
Nipponbare rice grown in Magenta pots in a 6 times diluted Hoagland solutions (with a layer of perlite to sustain the seed). Plants were inoculated with either nothing, Burkholderia vietnamiensis LMG10929, Paraburkholderia kururiensis M130 or Paraburkholderia phytofirmans PsJN. A RNA extraction of leaves and roots was performed at 7 day post inoculation (dpi), and RNAseq was done on polyA mRNAs, on three replicates per condition per organ. |
The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. |
| Gene expression profiling of reproductive meristem types in early rice inflorescences by laser microdissection |
We used a precise laser microdissection and RNA-sequencing approach in Oryza sativa ssp. japonica cv. Nipponbare to produce quantitative data that describe the landscape of gene expression in four different meristem types: the rachis meristem, the primary branch meristem, the elongating primary branch meristem (including axillary meristems), and the spikelet meristem. |
The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. |
| Genome Wild Expression in early reproductive stages in rice |
5 species of rices have been analyzed at the developmental stage (determinate and indeterminate stages) at three biological replicates: O. sativa japonica (Niponbarre), O. sativa Indica (IR64), O. rufipogon (W1654-2), O. glaberrima (Tog5681) and O. barthii (B88). For expression analysis, we collected 15 immature panicles each from at least 10 plants per accession, per stage, collected from 4 to 15 d after floral induction (i.e. transfer to short day conditions) for each biological replicate. For sample... read more |
The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. |
| Whole Genome Assembly and Annotation for Nerica4 | ||
| Whole Genome Assembly and Annotation for Nerica L19 | ||
| Whole Genome Assembly and Annotation of Oryza glaberrima |
Assembly The genome sequence was generated with PacBio technology and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717, deposited in Genbank with project accession number ADWL02000000. Annotation Protein-coding genes were annotated with MAKER-P software in CSHL. Source : Gramene |
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| Whole Genome Assembly and Annotation of Asian rice (Zhou et al, 2020) |
Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR... read more |
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| Genome sequencing and assembly of 12 rice varieties |
Genome assemblies from 12 rice varieties (https://doi.org/10.1038/s41597-020-0438-2) |
Sequence assembly capable on a very large scale such as assembly of whole genomes. [http://edamontology.org] |
Pages
Rice GH is a collaborative project among rice teams from IRD & CIRAD. Funding has been provided by CRP Rice, IRD and CIRAD
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