Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diurnal Regulation of Gene Expression in Leaves Over a 72-Hour Period

ABSTRACT: Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105K Agilent microarray to investigate diurnal rhythms. The top-most fully expanded leaf from each plant collected. Plants were sampled every 4 hours over 3 days. Our sampling times were: 6 am (dawn), 10 am, 2 pm, 6 pm, 10 pm and 2 am. Tissues were collected from three field reps and within each field rep we collected samples from three individual plants

ORGANISM(S): Zea mays

SUBMITTER: Kevin Hayes

PROVIDER: E-GEOD-23917 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period

Project description:Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles. A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105K Agilent microarray to investigate diurnal rhythms. The top-most immature ear, 4-5 cm in length, was collected. Plants were sampled every 4 hours over 3 days. Our sampling times were: 6 am (dawn), 10 am, 2 pm, 6 pm, 10 pm and 2 am. Tissues were collected from three field reps and within each field rep we collected samples from three individual plants

2010-09-02 | E-GEOD-23916 | biostudies-arrayexpress

Diurnal Regulation of Gene Expression in Leaves Over a 72-Hour Period

2010-09-02 | GSE23917 | GEO

Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period

2010-09-02 | GSE23916 | GEO

Diurnal Regulation of Gene Expression in Leaves and Immature Ears Over a 72-Hour Period

Project description:This SuperSeries is composed of the following subset Series: GSE23916: Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period GSE23917: Diurnal Regulation of Gene Expression in Leaves Over a 72-Hour Period Refer to individual Series

2010-09-02 | E-GEOD-23918 | biostudies-arrayexpress

The basal cm of leaf 4 of GA2OX::PLA1 (193-01) versus wild type in the growth chamber and the field (May-June 2015)

Project description:GA2OX::PLA1 transgenic plants and their none-transgenic siblings were grown in the field in Wetteren and in the growth chamber. In the field, we sampled three plants per plot (three plots were sown per genotype), resulting in three pools each consisting of three plants. Every pool represented a different subplot. In the growth chamber, the plants were sampled randomly across the population, with three pools, each consisting of three plants. For each plant, the day of leaf 4 appearance was marked and the samples were taken two days after leaf 4 appeared (DALA). The seedlings were cut just above soil level and the growing fourth leaf was dissected out and the younger leaves inside leaf 4 were removed. Using a ruler we sampled the basal cm of leaf 4 (division zone) for RNA preparation. The samples were snap frozen and transported to the lab for storage at -80 degrees and further processing. One time point was sampled, two days after leaf 4 appearance.

2019-10-16 | E-MTAB-8094 | biostudies-arrayexpress

Time-course in rice leaves in the field: WT (cv.Norin8) vs. osgi mutant

Project description:Diurnal time-course transcriptional profiling of rice leaf in the field comparing a circadian clock related mutant, osgi, with the wild-type (WT). Two sample experiments (WT vs. osgi) : 13 time-points (2h interval), 8 replicates (2leaves from individual plants x 4stages(each staggered by tranplanting dates with one week interval)): sampled on Aug. 12th 7:00-Aug.13th 7:00 (2008) at a paddy field in Tsukuba (Japan)

2011-05-18 | E-GEOD-18685 | biostudies-arrayexpress

The basal cm of leaf 4 of GA2OX::PLA1 (193-01) versus wild type in the growth chamber and the field (May-June 2016)

Project description:GA2OX::PLA1 transgenic plants and their none-transgenic siblings were grown in the field in Wetteren and in the growth chamber. In the field, we sampled three plants per plot (three plots were sown per genotype), resulting in three pools each consisting of three plants. Every pool represented a different subplot. In the growth chamber, the plants were sampled randomly across the population, with three pools, each consisting of three plants. For each plant, the day of leaf 4 appearance was marked and the samples were taken two days after leaf 4 appeared. The seedlings were cut just above soil level and the growing fourth leaf was dissected out and the younger leaves inside leaf 4 were removed. Using a ruler we sampled the basal cm of leaf 4 (division zone) for RNA preparation. The samples were snap frozen and transported to the lab for storage at -80 degrees and further processing. Two time points were sampled, two days after leaf 4 appearance as well as six days after leaf appearance.

2019-10-16 | E-MTAB-8095 | biostudies-arrayexpress

RNA-seq data on leaf 8 blade tissue of 62 individual Brassica napus (Darmor) plants grown in the field.

Project description:62 individual Brassica napus plants of the same accession grown in the same field were expression-profiled in autumn 2016 and phenotyped extensively until harvest in spring 2017. Machine learning models were used to link gene expression to the phenotypes of individual plants, with the purpose of assessing how much phenotype information in encoded in ‘noisy’ gene expression variation among individual plants of the same background grown under the same uncontrolled field conditions. Rosette leaf 8 blades of 62 individual Brassica napus plants of the same winter-type accession (BnASSYST-120, Darmor) grown in the same field (50°58'24.9\\"N 3°46'49.1\\"E, Merelbeke, Belgium) were RNA-seq profiled. No treatments or stresses were applied, all plants were profiled individually under uncontrolled field conditions. Sown at 2016-09-08, rosette leaf 8 sampled for RNA-seq at 2016-11-28, plants harvested at 2017-06-13.

2022-10-10 | E-MTAB-11904 | biostudies-arrayexpress

Wild and cultivated species of rice have distinctive proteomic responses to drought

Project description:Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7-d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis is responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Moreover, distinctive patterns of expression of proteins in drought were observed across the entire O. australiensis proteome. An intermediate impact of drought on photosynthetic and stress-response proteins is reported in O. glaberrima relative to O. sativa but the drought response was most striking in O. australiensis. For example, photosynthetic proteins decreased when O. sativa after drought, while a narrower range of stress-responsive proteins was up-regulated. Distinctive proteomic profiles and the expression levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes.

2021-09-09 | PXD019885 | Pride

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

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