Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of Gene Expression in Rice Shoot and Root

ABSTRACT: The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE50844 | GEO | 2013/09/14

SECONDARY ACCESSION(S): PRJNA219160

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Characterization of Gene Expression in Rice Shoot and Root

Project description:The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. The Phalanx microarray platform is based upon the hybridization of a single labeled sample (derived from RNA), followed by one-channel detection. The intensity of the hybridization signal is used to determine target concentration. In order to validate the technical quality of each probe in our arrays, we carried out 10 independent hybridizations on samples representing two different rice tissues – root and shoot. To examine the gene expression profiles between rice root and shoot development, total RNA extracted from rice root and shoot were processed on the rice OneArray® microarray following the standard protocol using five arrays for each tissue type. Raw expression data from 10 microarrays (e.g. 5 arrays × 2 tissues) were normalized and Pearson’s correlation coefficients were calculated for the data sets of hybridization signal intensities.

2013-09-14 | E-GEOD-50844 | biostudies-arrayexpress

Tiling microarray analysis of japonica and indica rice chromosome 10

Project description:This experiment was designed to identify transcribed regions of both japonica and indica rice chromosome 10. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 750,282 and 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogating the japonica and the indica chromosome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: other

2005-04-09 | GSE2500 | GEO

Metabolome analysis on multi-connected biparental chromosome segment substitution line populations in rice

Project description:rice flag leaves at heading stage from three chromosome substitution line populations, which were respectively constructed by introducing genomic segments from japonica cultivar Niponbare, indica cultivar Minghui 63 and wild accession ACC10, to an indica cultivar Zhenshan 97, were collected. Metabolomics profile was conducted to generate quantitative trait loci that may affect contents of metabolites, and candidate genes were assigned.

2018-08-06 | ST001031 | MetabolomicsWorkbench

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under cold stress and recovery stage

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 OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed

2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under salt stress and recovery stage

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 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 OneArrayï¼ v1. Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed

2016-06-30 | E-GEOD-76613 | biostudies-arrayexpress

Integrative approach for precise genotyping and transcriptomics of a salt tolerant introgression line in rice

Project description:Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines.

2021-12-20 | GSE167342 | GEO

Unique transcriptome and gene expression analysis of rice seedling reveals different cadmium response regulatory mechanisms between Indica and Japonica rice

Project description:Purpose: The goal of this study is to compare the different genetic mechanisms between Indica and Japonica rice under cadmium stress.

2023-01-02 | GSE196229 | GEO

Transcription profiling of rice under salinity stress

Project description:Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage Experiment Overall Design: Rice Genotypes a sensitive japonica, m103, tolerant japonica agami, sensitive indica ir29 and tolerant indica ir63731 were used for expression anlaysis using the tissue from crown and growing point under control and salt stressed conditions at the sensitive early reproductive stage (panicel initiation).

2008-11-05 | E-GEOD-4438 | biostudies-arrayexpress

Gene expression profiling of rice embryogenic calli after Agrobacterium infection

Project description:Agrobacterium tumefaciens-mediated genetic transformation has been routinely used in rice for more than a decade. However, the transformation efficiency of the indica rice variety is still unsatisfactory and much lower than that of japonica cultivars. Further improvement on the transformation efficiency lies in the genetic manipulation of the plant itself, which requires a better understanding of the underlying process accounting for the susceptibility of plant cells to Agrobacterium infection as well as the identification of plant genes involved in the transformation process. In order to investigate the related genes affecting the transformation efficiency of embryogenic calli of different rice cultivars, we used Affymetrix GeneChip® Rice Genome Array to measure the global gene expression profiling just before transformation and at four different time points after transformation (1 h, 6 h, 12 h, 24 h) in both japonica rice cultivar Nipponbare and indica rice cultivar Zhenshan 97.

2012-01-01 | GSE32426 | GEO

Expression data from rice varieties IRAT109 and ZS97 for drought stress treatment in flag leaves

Project description:Comparative transcriptional profiling of two contrasting rice genotypes,IRAT109 (drought-resistant japonica cultivar) and ZS97 (drought-sensitive indica cultivar), under drought stress during the reproductive stage

2011-11-05 | GSE25176 | 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