Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cool-responsive change in the rice anther transcriptome

ABSTRACT: The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains. The five rice strains exposed to the low temperature at 12Â°C for four days, were used for the microarray analyses. RNA was extracted from the anthers one day (C1), three days (C3) and five days (C5: this is one day after completion of the cool treatment) after the cool treatment and non-treated anthers (C0) with three biological replicates.

ORGANISM(S): Oryza sativa

SUBMITTER: Yuji Kishima

PROVIDER: E-GEOD-49561 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Cool-responsive change in the rice anther transcriptome

Project description:The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains.

2013-08-06 | GSE49561 | GEO

RNA sequencing of Nipponbare control and OsCNGC4, OsCNGC5 double knockout mutant in mature anthers

Project description:We created a double loss-of-function/knockout mutant targeting two rice genes simultaneously. The selected genes are as follows: OsCNGC4(LOC_Os03g44440) and OsCNGC5(LOC_Os12g28260). These two CNGCs are strongly transcriptional expressed in the rice mature anthers (stages 13-14). The mutant of these OsCNGC4/5 displayed a low seed-setting rate. This data refers to the transcriptome of mature anthers from the double mutant of OsCNGC4 and OsCNGC5. We sampled mature anther for the analysis.

2024-04-30 | E-MTAB-13943 | biostudies-arrayexpress

The transcriptome of anthers of rice gamyb mutant expressing various GAMYB homologs was measured at the microspore stage.

Project description:To confirm the function of the GAMYB homologs for Selaginella moellendorffii and Physcomitrella patens in rice cells, we examined the expression profile in the anthers of transgenic plants, which OsGAMYB, SmGAMYB, or PpGAMYB2 is expressed under the control of the rice GAMYB promoter in rice gamy mutant. Expression profiling was conducted using rice 4x44K microarray RAP-DB (G2519F#15241). The microarray was used to profile gene expression in OsGAMYB:OsGAMYB, OsGAMYB:SmGAMYB, OsGAMYB:PpGAMYB2 and vector transgenic plants. To assess the reproducibility of the microarray analysis, each microarray experiment was performed twice using RNA samples that had been isolated independently (i.e., two biological replicates), and included a dye-swapping test as a technical replicate for each biological replicate.

2011-11-07 | E-GEOD-32652 | biostudies-arrayexpress

Spatio-temporal gene expression of various tissues/organs throughout entire growth in rice

Project description:An overview of the expression pattern of all rice genes under natural field conditions based on microarray analysis of different organs and tissues at various stages of growth and development from transplanting to harvesting. A total of 48 samples representing organs/tissues at various stages of growth and development with 3 replicates each except for one anther sample with 2 replicates. Vegetative organs such as leaf blade, leaf sheath, root and stem were sampled during the vegetative, reproductive and ripening stages. Young inflorescence, anther, pistil, lemma, palea, ovary, embryo, and endosperm were sampled at various stages of development.

2011-01-13 | E-GEOD-21396 | biostudies-arrayexpress

Temperature-sensitive sterility in rice determined by the dual role of AGO1d in phasiRNA biogenesis and function

Project description:Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants. Monocots generate 21- and 24-nt phasiRNAs by miR2118 and miR2275 respectively from noncoding RNAs with spatial-temporal specificity during anther development. However, which ARGONAUTES (AGOs) associate with these two miRNAs remains elusive. Here we show that rice AGO1d, specifically expressed in anther wall cells before and during meiosis, associates with both miR2118 and miR2275 to mediate phasiRNA biogenesis. Furthermore, AGO1d also binds to miR2118-triggered 21-nt phasiRNAs preferentially with a 5’-terminal uridine, suggesting a dual role in phasiRNA biogenesis and function. Depletion of AGO1d causes reduction of 21- and 24-nt phasiRNAs and temperature-sensitive sterility. Anthers of the ago1d mutants at lower temperatures mainly display defects in tapetal cells and vacuolation during pollen formation. These results uncover an essential role of AGO1d in rice anther development at lower temperatures and demonstrate coordinative roles of AGO proteins during reproductive phasiRNA biogenesis and function

2022-08-30 | GSE191268 | GEO

Protein acetylation landscape of developing rice anthers

Project description:Protein lysine acetylation (KAC) is a dynamic and reversible post-translational modification, playing important biological roles in many organisms.Here, we reported results from a proteomic investigation to detect KAC status of the developing rice anthers near the time of meiosis (RAM), providing strong biochemical evidence for roles of many KAC-affected proteins during rice anther development and meiosis. We identified a total of 1,354 KAC sites in 676 proteins.

2019-03-06 | PXD007986 | Pride

RNA-Seq of wild type and osmtd2 mutant rice anthers

Project description:Rice anthers at anthesis stage from the wild type and osmtd2 mutant anther (Dongjin cultivar) We collected the sample from our field and immediately froze the samples with liquid nitrogen.

2021-06-30 | E-MTAB-10412 | biostudies-arrayexpress

RNA-Seq of Oryza sativa Dongjin (rice) wild type and gori mutant anthers

Project description:Rice anthers at anthesis stage from the wild type and gori mutant anther (Dongjin cultivar) We collected the sample from our field and immediately froze the samples with liquid nitrogen.

2020-11-03 | E-MTAB-9726 | biostudies-arrayexpress

RNA-Seq of wild type and tape-1 mutant rice anthers

Project description:Rice anthers at anthesis stage from the wild type and tape-1 mutant anther (Dongjin cultivar) We collected the sample from our field and immediately froze the samples with liquid nitrogen.

2022-12-31 | E-MTAB-10439 | biostudies-arrayexpress

RNA-Seq of wild type and MADS triple mutant anthers

Project description:Rice anthers at anthesis stage from the wild type and MADS triple mutant anther (Dongjin cultivar) We collected the sample from our field and immediately froze the samples with liquid nitrogen.

2022-01-01 | E-MTAB-11246 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data