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

DAP = Days After Pollination, RNAseq = RNA (cDNA) sequencing with Illumina, DGE = Digital Gene Expression

NSF Logo This work is supported by grants (DBI-0321538/DBI-0834043) from the National Science Foundation.