Rice Gene Expression
Next Generation Sequencing Transcriptome Data in the Rice Genome Annotation Project
Expression data were derived from NCBI Sequence Read Archive (SRA). Sequence reads were mapped to the version 7 pseudomolecules with Tophat (Trapnell, 2009). Expression abundances for RNAseq libraries were calculated with Cufflinks (Trapnell, 2010). Presence/absence expression values were assigned for digital gene expression (DGE) libraries, and genes were called 'expressed' if at least one sequence read mapped uniquely within an exon.
Download the complete expression data table for all rice genes.
Rice Expression Matrix File - Excel (.xls)
Rice Expression Matrix File - Zipped tab delimited text file (.txt.zip)
| Library Name | Library Description | Library Type | Rice Genotype |
|---|---|---|---|
| SRX100741 | Leaves-20 days | RNAseq | Nipponbare |
| SRX100743 | Post-emergence inflorescence | RNAseq | Nipponbare |
| SRX100745 | Pre-emergence inflorescence | RNAseq | Nipponbare |
| SRX100746 | Anther | RNAseq | Nipponbare |
| SRX100747 | Pistil | RNAseq | Nipponbare |
| SRX100749 | Seed-5 DAP | RNAseq | Nipponbare |
| SRX100753 | Embryo- 25 DAP | RNAseq | Nipponbare |
| SRX100754 | Endosperm- 25 DAP | RNAseq | Nipponbare |
| SRX100755 | Seed- 10 DAP | RNAseq | Nipponbare |
| SRX100756 | Endosperm- 25 DAP (replicate) | RNAseq | Nipponbare |
| SRX100757 | Leaves- 20 days (replicate) | RNAseq | Nipponbare |
| SRR042529 | Shoots | RNAseq | Nipponbare |
| SRX016113 | Seedling four-leaf stage | RNAseq | F1 93-11/Nipp |
| SRX016112 | Seedling four-leaf stage | RNAseq | F1 Nipp/93-11 |
| SRX016111 | Seedling four-leaf stage | RNAseq | 93-11 |
| SRX016110 | Seedling four-leaf stage | RNAseq | Nipponbare |
| SRR074128 | M.oryzae infected-Resistant-6h | DGE | Nipponbare |
| SRR074129 | M.oryzae infected-Resistant-12h | DGE | Nipponbare |
| SRX032224 | M.oryzae infected-Resistant-24h | DGE | Nipponbare |
| SRR074133 | M.oryzae infected-Susceptible-6h | DGE | Nipponbare |
| SRR074134 | M.oryzae infected-Susceptible-12h | DGE | Nipponbare |
| SRR074135 | M.oryzae infected-Susceptible-24h | DGE | Nipponbare |
| SRR074136 | M.oryzae infected-Susceptible-96h | DGE | Nipponbare |
| SRX032221 | Mock treatment-24hr | DGE | Nipponbare |
| SRR074137 | Callus-35 days | DGE | Nipponbare |
| SRR074139 | Cold Stress-Leaves-2wks | DGE | Nipponbare |
| SRR074140 | Cold Stress-Roots-2wks | DGE | Nipponbare |
| SRR074142 | Drought Stress-Leaves-2wks | DGE | Nipponbare |
| SRR074143 | Drought Stress-Roots-2wks | DGE | Nipponbare |
| SRR074149 | Salt Stress-Leaves-2wks | DGE | Nipponbare |
| SRR074150 | Salt Stress-Roots-2wks | DGE | Nipponbare |
| SRR074153 | Untreated-leaves-2wks | DGE | Nipponbare |
| SRR074154 | Untreated-Roots-2wks | DGE | Nipponbare |
| SRR074156 | Rice leaf-beet armyworm damaged-24h | DGE | Nipponbare |
| SRR074158 | Rice leaf- Mechanical damaged-24h | DGE | Nipponbare |
| SRR074160 | Rice leaf-Water weevil damaged-24h | DGE | Nipponbare |
| SRR074144 | Germinating seed-3 days | DGE | Nipponbare |
| SRR074145 | Immature panicle-90 days | DGE | Nipponbare |
| SRR074146 | Mature leaves-60 days | DGE | Nipponbare |
| SRR074147 | Mature pollen | DGE | Nipponbare |
| SRR074151 | Stem-60 days | DGE | Nipponbare |
| SRR074170 | Mature Sigma and Ovary | DGE | Nipponbare |
| SRR074171 | Mature roots-60days | DGE | Nipponbare |
| SRR074161 | HighMilling-Developing seeds-6days | DGE | Cypress |
| SRR074163 | HighTaste-Developing seeds-6days | DGE | Ilpumbyeo |
| SRR074164 | LowMilling-Developing seeds-6days | DGE | LaGrue |
| SRR074167 | Control-Developing seeds-6days | DGE | Nipponbare |
| SRR074169 | LowTaste-Developing seeds-6days | DGE | YR15965 |
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This work is supported by grants (DBI-0321538/DBI-0834043) from the National Science Foundation. |