Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression dynamics in rice peduncles at the heading stage

ABSTRACT: We report transcriptome profiling of elongating and non-elongating peduncles of rice in two Indian cultivars, Swarna and Pokkali at the time of heading. Sequencing of twelve libraries (three replicates from each stage) yielded >6.9 billion paired-end reads.

ORGANISM(S): Oryza sativa

PROVIDER: GSE157727 | GEO | 2020/12/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptomes of Rice internode before and after heading

2013-10-01 | GSE51289 | GEO

Transcriptomes of Rice internode before and after heading

Project description:To identify genes that co-express with rice cellulose synthase genes involved in rice secondary cell wall formation, transcriptome analyses was performed using rice internodesbefore and after the heading stage, where secondary cell wall formation extensively occur. Transcriptomes of rice third or the fourth internodes were analyzed at 17, 8, and 1 day before, and 6, 13, and 35 days after heading Please note that the current data were normalized together with additional 143 sample data available in GEO and the list of the sample accessions is provided in Series supplementary file [normalized_together_GSMs.txt].

2013-10-01 | E-GEOD-51289 | biostudies-arrayexpress

Single-base resolution DNA methylation maps of rice cultivars under control and stress conditions

Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants. Whole genome bisulfite sequencing of seven control/stressed samples from three rice cultivars (IR64, N22 and Pokkali)

2015-12-31 | E-GEOD-60288 | biostudies-arrayexpress

Analysis of the transcriptomes of salt tolerant and susceptible cultivars of indica rice by microarray

Project description:Over the years, many traditional rice varietites of India were sourced and studied owing to their ability to withstand abiotic pressures like excessive salinity in the soil and water. These cultivars growing in specific areas of the country represent a rich gene pool from where a deeper understanding of the processes underlying tolerance to abiotic stress can be gained. Indigenous varieties like Nonabokra and Pokkali are known salt tolerant varieties and are being studied in great detail. In the present study, we have analyzed the transcriptomes of the contrasting cultivars; Nonabokra (tolerant), Pokkali (tolerant) and IR29 (susceptible) in order to decipher the differences in their responses to salinity stress by utilizing microarray.

2021-12-31 | GSE41650 | GEO

RNA-seq of seeds of Dongjin, Heukseol and Jeokjinju at 20 days after heading

Project description:For gene expression analysis, RNA-seq was performed in seeds of Dongjin (white rice), Heukseol (black rice) and Jeokjinju (red rice) at 20 days after heading

2023-03-24 | E-MTAB-9993 | biostudies-arrayexpress

Differential gene expression analysis of maize leaf at heading stage in response to water-deficit stress

Project description:Periods of soil water deficit could occur at any time during the crop season, but maize is particularly sensitive to water stress around flowering time. At this time the stress usually causes remarkable yield loss. Heading time, which is just before tassel flowering, is one of the most important stages that maize productivity would be affected severely if plants encounter water stress. The whole-genomic gene expression changes of maize plants in response to water deficit stress at this stage have not been studied. The present work utilized an Arizona Maize Oligonucleotide Array Version 1.9，which was consisted of A and B slides carrying with a total of 57,452 maize 70-mer oligonucleotides, was used to monitor gene expression profile changes in maize leaves subjected to 1 day and 7 days water-deficit stress respectively at the heading stage. Keywords: stress response

2008-02-25 | GSE10596 | GEO

Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations

Project description:Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations

| PRJNA1105855 | ENA

Stress responsive gene expression in rice cultivars

Project description:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.

2015-12-31 | GSE60287 | GEO

Next Generation Sequencing of non-heading Chinese cabbage (Brassica rapa ssp. chinensis)

Project description:Next-generation sequencing has been applied on seedling of two genotypes of noheading Chinese cabbage, Huaq and Wut. The goals of this study are to compare the different expression of small RNAs which is possible effect the phynotype of close genetic relation cultivars.

2014-06-14 | GSE38722 | GEO

Fumarylacetoacetate hydrolase targeted by a Fusarium graminearum effector positively regulates wheat FHB resistance and yield and promotes heading

Project description:Fusarium head blight (FHB), caused by Fusarium graminearum is a devastating disease that affects global wheat production. F. graminearum encodes many effector proteins; however, its virulence mechanisms are poorly understood. In this study, we identified a secretory effector candidate protein (FgEC10) that is essential for the virulence of F. graminearum and suppresses the basal immune response. FgEC10 interacted strongly with wheat fumarylacetoacetate hydrolase (TaFAH) and accelerated its degradation via the 26S proteasome pathway. In addition, we showed that TaFAH interacted with TaPSMD, an important component of the 26S proteasome and that FgEC10 enhanced the interaction between TaFAH and TaPSMD. RNA silencing or overexpression of TaFAH in wheat plants showed that TaFAH positively regulated wheat FHB resistance, heading period, and grain yield. Transcriptomic analysis revealed that TaFAH promoted the expression of genes associated with disease resistance and the heading period. Metabolomic analysis revealed that overexpression of TaFAH increased the levels of several amino acids that inhibited F. graminearum growth and enhanced wheat resistance to FHB. Collectively, our study reveals a novel pathogenic mechanism and provides a valuable genetic resource for improving FHB resistance and grain yield in wheat.

2024-08-15 | GSE254427 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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