Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq to investigate the transcriptional Response to drought stress in two Indica rice varieties Nagina22 and Nonabokra

ABSTRACT: We designed a time series experiment in order to better understand acclimation and avoidance responses of two different Indica rice varieties Nagina22, a drought tolerant, and Nonabokra, a saline tolerant.We generated RNA-Seq transcriptome data for treated and untreated samples, with three biological replicates, per time point for drought response, an environmental stress experiment.The data generated was analyzed by calling polymorphisms, expression levels and eventually curate gene network pathways specific to the landraces’ genetic background and tolerance level.

INSTRUMENT(S): Illumina HiSeq 3000

ORGANISM(S): Oryza sativa Indica Group

SUBMITTER: Noor Al-Bader

PROVIDER: E-MTAB-7317 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq analyses of most resistance Indica Rice varieties (Oryza sativa L.) leaves tissue under water-deficit condition

Project description:In order to evaluate the genome differences and find the more tolerant cultivar, first eleven Malaysian rice cultivars namely, MR219, MR276, MR220, MR211, MR219-4, MR253, Q50, Q74, MR159, Masuri and MR263 were subjected under water deficit. Then, based on the morphological and physiological traits, the more drought-tolerant and -susceptible cultivars were screened and time-course gene expression profiling established by a comprehensive transcriptome database sequencing of the leaf RNA of tolerant rice. The current investigation provides pivotal data for understanding the rice drought tolerance mechanisms.

2017-07-27 | E-MTAB-5402 | biostudies-arrayexpress

Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease

Project description:Rice is the major staple food for more than half of world's population. As global climate changes, we are observing more floods, droughts and severe heat waves. Two rice cultivars with contrasting genetic backgrounds and levels of tolerance to drought, Nipponbare and IAC1131, were used in this study. Four-week-old seedlings of both cultivars were grown in large soil volumes and then exposed to moderate and extreme drought for 7 days, followed by 3 days of re-watering. Mature leaves were harvested from plants from each treatment for protein extraction and subsequent shotgun proteomic analysis, with validation of selected proteins by western blotting. Gene Ontology (GO) annotations of differentially expressed proteins provide insights into the metabolic pathways that are involved in drought stress resistance. Our data indicate that IAC1131 appears to be better able to cope with stressful conditions by up regulating a suite of stress and defence response related proteins. Nipponbare, in contrast, lacks the range of stress responses shown by the more stress tolerant variety, and responds to drought stress by initiating a partial shutdown of chlorophyll biosynthesis in an apparent attempt to preserve resources.

2016-09-15 | PXD004096 | Pride

2018-01-31 | PXD004118 | Pride

Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue and during fibre development stages.

Project description:This SuperSeries is composed of the following subset Series: GSE29566: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue. GSE29567: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress during fibre development stages. Refer to individual Series

2012-06-03 | E-GEOD-29810 | biostudies-arrayexpress

Genetic Engineering of indica Rice with AtDREB1A Gene for enhanced Abiotic Stress Tolerance

Project description:Global gene expression analysis of AtDREB1A transgenic rice line (TL4) at reproductive stage under drought stress was conducted using microarray to explore the drought stress-responsive transcription pathways. Drought stress was imposed at late vegetative stage till booting of the plants. Flag leaf was collected on 14th day of the drought stress. Drought stress was imposed on T3 plants of two homozygous transgenic rice events of PS2 and NT plants by withholding irrigation for 14 days in the National Phytotron Facility, IARI.

2018-04-29 | E-MTAB-5700 | biostudies-arrayexpress

Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress during fibre development stages.

Project description:Transcriptome analysis in cotton during fibre development stages. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out at fibre development stages (0, 5, 10 and 20 dpa/Days post anthesis). Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome. Total RNA was isolated from 0 dpa, 5 dpa, fibre bearing ovules of 10 dpa, and fibre bearing ovules of 20 dpa. Samples were collected from both drought induced and control plants. Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following the Affymetrix protocols. Three biological replicates were maintained.

2012-06-03 | E-GEOD-29567 | biostudies-arrayexpress

Whole genome-wide expression profiles of hemp (Cannabis sativa L.) in response to drought stress

Project description:Drought stress is the main environmental factor influencing hemp growth and yield. However, little is known about the response mechanism of hemp to drought stress. A total of 44.10 M tags and 8.91G bases were sequenced in the control hemp (CK) and drought stress hemp (DS) libraries. A total of 1292 differentially expressed genes (DEGs), including 883 up-regulated genes and 409 down-regulated genes, were identified. These results may contribute toward improving our understanding about the drought stress regulatory mechanism of hemp, and improving its drought tolerance ability. 3' tag-based DGE libraries were generated to exam the differentially expressed gene between drought-stressed and well-watered hemp

2017-04-22 | E-GEOD-56964 | biostudies-arrayexpress

Gene expression profiling of acute drought response in leaf and root of rice

Project description:In this research, an array of 27,448 rice genes was used to elucidate gene expression in air-dried rice seedlings (lead and root) at various periods of treatment times. The analyses show that rice responds to drought stress mainly by down-regulating many biological processes including gene expression and regulation, protein phosphorylation, and cellular metabolism. Among strategies to actively adapt to drought, most significant are inducing protective molecules, which may be differentially regulated based on plant organs. A total of 20 chips was used for the microarray analysis. Total RNAs were extracted from leaf and root of rice seedlings that had undergone 0-12 hrs acute drought. Experiments were duplicated. The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.dna.affrc.go.jp/).

2012-09-21 | E-GEOD-38130 | biostudies-arrayexpress

Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue.

Project description:Transcriptome analysis in cotton under drought stress. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out in leaf tissue. Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Leaf samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome. Total RNA was isolated from leaf tissue. Samples were collected from both drought induced and control plants. Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following the Affymetrix protocols. Three biological replicates were maintained.

2012-06-03 | E-GEOD-29566 | biostudies-arrayexpress

Identification of drought responsive genes at reproductive stage in upland rice variety Nagina22 through comparative microarray analysis

Project description:In the current study we did microarray of upland rice cultivar Nagina22 for drought stress at reproductive stage (panicle initiation) and analyzed drought stress responsive genes. We have taken flag leaf for our study as it is most essential organ for photosynthesis in rice. Normal watering Vs Drought Stress Flag leaf of Control (Three biological replicates) plant of Nagina22: C1, C2, C3 Flag leaf of drought stressed (Three biological replicates) plant of Nagina 22: S1, S2, S3

2017-12-25 | E-MTAB-4994 | 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