Express data from rice endosperm
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE26840 | GEO | 2011/12/06
SECONDARY ACCESSION(S): PRJNA142021
REPOSITORIES: GEO
Similar Datasets
Project description:Immatured rice seeds 7-8 days after pollination were used for expression analysis and matured rice leaf was used as control. Targets from biological replicates of both were generated and the expression were determined using Affymetrix Rice Genome arrays. Rice immatured seed after 7-8 days pollination were selected of early development for RNA extraction and hybridization on Affymetrix microarrays. Matured rice leaf was set as control. Each with 3 replicates were analyzed.
2011-12-06 | E-GEOD-26840 | biostudies-arrayexpress
Project description:We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development. Rice embryo and endosperm were selected for DNA extraction and methylacytosine immunoprecipetation combined with Illumina sequencing. We sought to obtain the genome-wide DNA methylation profilings of embryo at 3,6,9 days after pollination(DAP) and endosperm at 2,3,6,9 DAP. To that end, we hand-selected embryo at 3,6,9 DAP and endosperm at 2,3,6,9 DAP according to morphological criteria.
2015-09-01 | E-GEOD-57706 | biostudies-arrayexpress
Project description:We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of regulated genes during this process. Rice endosperm at 2 days after pollination(DAP) was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the endosperm expression profile at 2 DAP. To that end, we hand-selected endosperm according to morphological criteria at 2 DAP before cellularization.
2015-09-01 | E-GEOD-57615 | biostudies-arrayexpress
Project description:rs10-02_ros_dme - genes regulated by ros and dme - Genes regulated by ros/dme? - Seeds of Col x ROS-/-/DME+/- 3 and 6 days after pollination (DAP) were harvested. Seeds of the cross Col x Col (3 and 6 DAP) were used as a control.
2011-06-02 | GSE29626 | GEO
Project description:We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development.
2015-09-01 | GSE57706 | GEO
Project description:We performed expression profiling experiments on two-week old rice leaf tissues grown in light and dark condition with the rice 47k array. Four biological replicates and a dye-swap were used. To generate more consistent results on light vs dark response in rice, biological replicates were prepared from 4 different varieties such as Kitaake, Nipponbare, Tapei309 and IR24 because individual genetic background can affect to expression profile (Townsend et al., 2003). Gene expression was assayed by probing the microarray with pooled Cy3 and Cy5 labeled cDNAs derived from 0.5-1.0ug high quality mRNA prepared from leaf samples. Keywords: Direct comparison
2008-09-07 | GSE8261 | 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:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from salt stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.
2016-06-30 | GSE76613 | GEO
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.
2014-10-15 | GSE57895 | GEO
Project description:The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). In this research, an array of 27,448 rice genes was used to elucidate the transcriptome of 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination) using a rice 3â² ORF tilling microarray. The ratio of standard deviation to the mean of microarray intensities was used to distinguish between organ-specific and constitutively expressed genes. Accordingly, the genes are classified into highly variable, variable, and constitutive groups. To isolate the organ-specific promoters, several genes were selected and validated in planta using reporter gene analysis. We found that the Os01g0702500, Os11g0211800, and Os01g0257300 promoters were active in the calli, germinating seeds, and roots, respectively. The Os08g0135500 promoter was shown to drive transgene expression in various organs of the mature flowers, such as the anther, lemma, and palea, whereas the Os03g0369100 promoter was only active in the anther. Lastly, the Os09g0553100 promoter induced high levels of reporter gene expression in all organs. The gene expression data from representative organs could put a frame work for large dataset collections and then subsequent profiling by subdivision of organ/tissues might be more efficient to find appropriate promoters. A total of 14 chips were used for microarray. Total RNAs were extracted from rice 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination. Experiments were duplicated.
2016-07-28 | E-GEOD-84903 | biostudies-arrayexpress