Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA105837 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression profiles of protein coding genes were characterized using Affymetrix rice genome array to compare with expression profiles of miRNAs. Experiment Overall Design: Five tissues (embryo, endosperm, leaf and root of 7-day-old seedlings, 10-day-old seedling) were analyzed, each has two biological repeats.
2009-02-08 | E-GEOD-11966 | biostudies-arrayexpress
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:Expression data from rice embryo and endosperm development
| PRJNA137875 | ENA
Project description:This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells). Keywords: tiling array, genome-wide transcription
2007-02-21 | GSE6996 | GEO
Project description:The analysis of gene expression during wheat development:; Gene expression measurements were carried out on a developmental tissue; series for wild-type wheat (cv. Chinese Spring) using the Affymetrix; Wheat GeneChip. Thirteen tissues at defined developmental stages were; chosen to match the barley (cv. Morex) tissue series of Druka et al. 2006 that used the Affymetrix Barley1 GeneChip. Three replicates of:; root tissue at two different developmental stages, leaf, crown,; caryopsis, anther, pistil, inflorescence, bracts, mesocotyl, endosperm,; embryo and coleoptiles were hybridised. Comparisons between this wheat; data and the barley dataset were performed and are available at; http://contigcomp.acpfg.com.au ; [PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tim Sutton. The equivalent experiment is TA3 at PLEXdb.] Experiment Overall Design: tissue type: germinating seed, coleoptile(3-replications); tissue type: germinating seed, root(3-replications); tissue type: germinating seed, embryo(3-replications); tissue type: seedling, root(3-replications); tissue type: seedling, crown(3-replications); tissue type: seedling, leaf(3-replications); tissue type: immature inflorescence(3-replications); tissue type: floral bracts, before anthesis(3-replications); tissue type: pistil, before anthesis(3-replications); tissue type: anthers, before anthesis(3-replications); tissue type: 3-5 DAP caryopsis(3-replications); tissue type: 22 DAP embryo(3-replications); tissue type: 22 DAP endosperm(3-replications)
2009-08-15 | E-GEOD-12508 | biostudies-arrayexpress
Project description:Cellularization is a key event during the development of the endosperm. Our understanding of the developmental regulation of cellularization has been limited for plants other than Arabidopsis. We found that the activation of OsbZIP76 coincided with the initiation of cellularization of rice. Either knockdown or knockout of OsbZIP76 led to precocious cellularization. Many genes involved in endosperm development or starch biosynthesis were prematurely activated in the caryopsis at two days after fertilization. The results implied that OsbZIP76 is involved in the regulation of cellularization in rice. As a putative transcription factor, OsbZIP76 alone lacked transcriptional activation activity. However, it was able to interact with OsNF-YB9 and OsNF-YB1, two nuclear factor Y (NF-Y) family transcription factors, both in yeast and in planta. OsbZIP76 and OsNF-YB9 showed similar endosperm-preferential expression patterns and the transiently expressed proteins were colocalized in the epidermal cells of tobacco. As with osnf-yb1 mutants, the osbzip76 mutants showed reduced seed size and reduced apparent amylose content of the seeds. We also confirmed that OsbZIP76 is an imprinted gene in rice, the expression of which depended on the genetic background. Our results suggested that OsbZIP76 is an endosperm-expressed imprinted gene to regulate development of the endosperm in rice.
2019-12-28 | GSE139445 | GEO
Project description:In angiosperms, stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. However, little is known about genes that regulate these processes in rice. Here we generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array. In total, we identified 665 probe sets (550 genes) to be expressed specifically or predominantly in the stigma papillar cells of rice. Real-Time quantitative RT-PCR analysis of 34 selected genes confirmed their stigma-specific expression. The expression of five selected genes was further validated by RNA in situ hybridization. Gene annotation shows that several auxin-signaling components, transporters and stress-related genes are significantly overrepresented in the rice stigma gene set. We also found that genes involved in cell wall metabolism and cellular communication appear to be conserved in the stigma between rice and Arabidopsis. Our results indicate that the stigmas appear to have conserved and novel molecular functions between rice and Arabidopsis. Experiment Overall Design: We generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array.
2008-11-08 | E-GEOD-7951 | biostudies-arrayexpress
Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages and two different tissues, embryo and endosperm of rice seeds with profile of RNA-seq. Methods: Oryza sativa. L mRNA profiles of two different ecotypes with 3 different maturation stages and 2 different tissues were generated by NGS, in duplicate, following Illumina NGS workflow. qRT–PCR validation was performed using SYBR Green assays. Results: We found the differentially expressed genes (DEGs) between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. In DEGs, gene ontology (GO) analysis and Mapman analysis were performed, and we discovered genes related to plant hormones and heat stress, which are not yet reported. These genes were validated through qRT-PCR, and it is likely to be highly related to seed dormancy. Conclusions: Our study represents the analysis of rice seed transcriptomes under two different ecotypes, three different seed maturation stages and two different tissues (Embryo and endosperm). Our results show that seed dormancy is affected and regulated by a plant hormones and heat stress. This study might provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.
2021-05-07 | GSE174017 | GEO