Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Baltazar Antonio

PROVIDER: E-GEOD-21396 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

RiceFREND: a platform for retrieving coexpressed gene networks in rice.

Sato Yutaka Y Namiki Nobukazu N Takehisa Hinako H Kamatsuki Kaori K Minami Hiroshi H Ikawa Hiroshi H Ohyanagi Hajime H Sugimoto Kazuhiko K Itoh Jun-Ichi J Antonio Baltazar A BA Nagamura Yoshiaki Y

Nucleic acids research 20121124 Database issue

Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions. Coexpression analysis of 27 201 genes was performed against 815 microarray data derived from expression profiling of various organs ...[more]

PMID: 23180784

Publication: 1/2

Similar Datasets

Diurnal and circadian gene expression profile of root throughout the entire growth of rice in the field

Project description:A continuous gene expression profiling of roots was performed at regular interval during a 48-hr period in 2 different growth stages to characterize the diurnal and circadian gene expression profile of rice growth under natural field conditions. Root was collected at 2-hr intervals during a 48-hr period at 2 different growth stages corresponding to early and late vegetative stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

2012-12-03 | E-GEOD-39423 | biostudies-arrayexpress

Diurnal and circadian gene expression profile of leaf throughout the entire growth of rice in the field

Project description:A continuous gene expression profiling of leaves was performed at regular interval during a 48-hr period in 9 different growth stages from transplanting until harvesting to characterize the diurnal and circadian gene expression profile of rice and to understand the transcriptional program and physiological state throughout entire the growth under natural field conditions. The uppermost fully expanded leaf in the main stem was collected at 2-hr intervals during a 48-hr period at 9 different growth stages encompassing the vegetative, reproductive and ripening stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

2012-12-03 | E-GEOD-36040 | biostudies-arrayexpress

Transcriptomic analysis of rice

Project description:This SuperSeries is composed of the following subset Series: GSE21396: Spatio-temporal gene expression of various tissues/organs throughout entire growth in rice GSE21397: Continuous gene expression profile of leaf throughout the entire growth in rice GSE21398: Comparison of gene expression profile of flag leaf from fertile and sterile lines of rice Refer to individual Series

2011-01-13 | E-GEOD-21494 | biostudies-arrayexpress

Gene expression profile of inflorescence at early developmental stage

Project description:Gene expression profiling of infrorescence was performed to obtain overall signature of transcriptome at early developmental stages of inflorescence. After the reproductive stage transition, inflorescence samples corresponding to the early stages of development were collected based on the size. We obtained inflorescence samples ranging from 0.6 to 10 mm in two replicates representing 8 stages in inflorescence development. A total of 16 microarray data were obtained.

2012-12-03 | E-GEOD-39426 | biostudies-arrayexpress

Developing endosperm: Nipponbare vs NIL(TGW6)

Project description:Gene expression profoling of developping endosperm at 3 and 6 days after flowering (DAH): Nipponbare vs NIL(TGW6) We used two rice varieties, NIL(TGW6) and Nipponbare.NIL(TGW6) is a nearly isogenic line containing the thousand grain weight qTGW6. For samples used three stages: 3 and 6 DAH endosperm in both Nipponbare and NIL(TGW6). Two dye swapped experiments were performed.

2013-02-12 | E-GEOD-44223 | biostudies-arrayexpress

Continuous gene expression profile of leaf throughout the entire growth in rice

Project description:A continuous gene expression profiling of leaves at regular interval from transplanting until harvesting was performed to understand the changes of transcriptional program and physiological state throughout entire growth of the rice plant. For continuous gene expression profile of leaf, the uppermost fully-expanded leaf, 1st leaf before 83 days after transplanting (DAT) and flag leaf from then on, in the main stem was sampled at 12:00 PM at regular intervals of 7 days encompassing 17 different growth stages with three replicates.

2011-01-13 | E-GEOD-21397 | biostudies-arrayexpress

Continuous gene expression profile of root at daytime throughout the entire growth of rice in the field

Project description:A continuous gene expression profiling of roots was performed during daytime at regular interval from transplanting until harvesting to characterize the transcriptional and physiological changes in the root system of rice throughout the entire growth under natural field conditions. Roots were sampled at daytime (12:00) at 7-day intervals encompassing 14 different growth stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

2012-12-03 | E-GEOD-39424 | biostudies-arrayexpress

Continuous gene expression profile of root at nighttime throughout the entire growth of rice in the field

Project description:A continuous gene expression profiling of roots was performed during nighttime at regular interval from transplanting until harvesting to characterize the transcriptional and physiological changes in the root system of rice throughout the entire growth under natural field conditions. Roots were sampled at nighttime (24:00) at 7-day intervals encompassing 14 different growth stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

2012-12-03 | E-GEOD-39425 | biostudies-arrayexpress

Continuous gene expression profile of leaf at nighttime throughout the entire growth of rice in the field

Project description:A continuous gene expression profiling of leaves was performed during nighttime at regular interval from transplanting until harvesting to understand the changes of transcriptional program and physiological state throughout entire growth of the rice plant under natural field conditions. The uppermost fully-expanded leaf in the main stem corresponding to the 1st leaf until 83 days after transplanting (DAT) and the flag leaf from them on were sampled in two replicates at 12:00 midnight at 7- day intervals encompassing 17 different growth stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.

2012-12-03 | E-GEOD-36042 | biostudies-arrayexpress

Comparison of gene expression profile of flag leaf from fertile and sterile lines of rice

Project description:To examine the role of formation of a strong sink during leaf senescence, we compared the expression profile of the flag leaf of three different sterile mutant lines with fertile plants. The fertile and sterile lines showed basically similar expression profiles of flag leaves sampled at the same time. However, the fertile lines showed more rapid and enhanced change in transcriptome as compared to the sterile lines indicating that leaf senescence initiated independent of sink formation and is accelerated by sink formation. Three independent mutant lines, namely, pair1, pair2, and mel1-1, and fertile plants (homozygous or heterozygous) derived from each segregating population were used for comparison. The flag leaves were sampled at initiation of heading, 1 week after heading (WAH), 2 WAH, and 3 WAH, with three biological replicates.

2011-01-13 | E-GEOD-21398 | 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