Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Eui-Jung Kim

PROVIDER: E-MTAB-13943 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA sequencing of Oryza sativa japonica control and OsRALF17/19 knockout mutant in mature rice anthers

Project description:Pollen tube growth is essential for successful fertilization and stable crop yields. We constructed loss-of-function/knock-out mutants that simultaneously target two rice genes using the CRISPR/Cas9 mutagenesis system. The selected OsRALF17 and OsRALF19 genes are strongly expressed in rice bicellular/tricellular pollen and have essential functions in the pollen tube growth. For the corresponding transcriptomic analysis, we sampled mature pollen anthers from a control group and an OsRALF17/19 knock-out mutant.

2023-09-29 | E-MTAB-12295 | biostudies-arrayexpress

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

Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton [degradome]

Project description:In this study, in order to identify miRNA targets, a degradome library derived from anthers of the WT and GMS (Genetic Male Sterility) mutant representing three stages of development was constructed and sequenced, resulting in the generation of 24.6 million raw reads. After removal of low quality sequences and adapter sequences, 24.4 million clean reads were obtained and 98% were 20 or 21 nt in length as expected in that normally length distribution peak of degradome fragment is between 20 and 21 nt [Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ: Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 2008, 18:758-762]. Identification of miRNA targets in the WT and GMS muant anthers. Anthers of the WT and GMS mutant representing three stages of development [the meiosis stage (WT: Mar-F-1; mutant: Mar-S-1) and tetrad stage (WT: Mar-F-2; mutant: Mar-S-2), together with the uninucleate microspore stage (WT: Mar-F-3; mutant: Mar-S-3) from the GMS M-bM-^@M-^XDong AM-bM-^@M-^Y mutant and its fertile wild type] were collected during early mornings.

2013-07-28 | E-GEOD-43389 | biostudies-arrayexpress

Comparison of transcriptome profile between wild-type and dao mutant plants

Project description:We identified and characterized that the rice Dioxygenase for Auxin Oxidation (dao) mutant displays pleiotropic phenotypes, including indehiscent anthers, sterile pollens, and increased free IAA levels in anthers.We conclude that DAO-mediated auxin catabolism is essential for auxin homeostasis and later stages of plant reproductive development, including anther dehiscence, and pollen viability. We used microarrays to identify differentially expressed genes in dao. For genome-wide expression analysis of dao, three replicates of WT and dao samples (RNA from mature anthers) were analyzed on Affymetrix Genechip® Rice Genome arrays by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer’s protocols. Genes showing a 2-fold change with a q-value ≤ 0.05 were considered to be differentially expressed.

2012-09-25 | E-GEOD-41097 | biostudies-arrayexpress

Transcription profiling of Arabidopsis early anther

Project description:We performed microarray experiments with RNAs from dissected immature anthers (stages 4-7) from wild-type, dyt1 and ams mutant plants, using the Affymetrix ATH1 chip. Experiment Overall Design: Anthers from Arabidopsis thaliana were selected at 4-7 stages of early development for RNA extraction and hybridization on Affymetrix microarrays. Samples from two mutants and wild-type anther.

2009-09-25 | E-GEOD-18225 | biostudies-arrayexpress

RNA sequencing of rice root in salt stress condition (250mM NaCl treatment)

Project description:Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.

2021-06-15 | E-MTAB-10653 | biostudies-arrayexpress

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