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

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Zea mays

SUBMITTER: Hilde Nelissen

PROVIDER: E-MTAB-8095 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

RNA-seq analysis of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants, profiled at different time points after leaf appearance and with different watering conditions

Project description:Transcriptome of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants was profiled at different days after leaf appearance (DALA). Leaf samples were taken for well-watered and water deficit plants at 4, 5, 6 and 7 days after the appearance of leaf four and at day 5 and 7, samples were harvested from the plants re-watered (RW) at day 4 (RW5) and day 6 (RW7), respectively. RIL89 is derived from a cross between parental lines B73 and H99.

2023-03-01 | E-MTAB-7749 | biostudies-arrayexpress

Diurnal Regulation of Gene Expression in Leaves 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 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

2010-09-02 | E-GEOD-23917 | biostudies-arrayexpress

Developmental profiling study along the maize leaf gradient

Project description:Transcriptome of three zones (from the base to 3.5 cm, from 3.5 to 7.0 cm and from 7.0 to 10.5 cm) of the developing fourth leaf of maize B104 plants was profiled at two days after leaf appearance (DALA). Only leaf samples were taken for well-watered plants.

2021-11-17 | E-MTAB-11108 | 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

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

Next Generation Sequencing Facilitates Small RNA Mediated Rice Resistance to Xoo

Project description:Purpose: The goal of this study is to identify small non-conding RNAs which are involved in rice resistance to Xoo. Methods: Rice leaves were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). And then, total RNA was extracted to be sequenced using Illumina GAIIx. Results: Using an optimized data analysis workflow to count the expression level of small ncRNA, we found several differentially expressed small ncRNA which may be participated in the interaction between rice and Xoo. Conclusions: Small ncRNA have be found to function in a variety of biological processes. Our study here has showed that several candidate miRNA or siRNA may play a significant role in rice immunity. Plants were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). Samples were collected before inoculation (ck) and at 2, 4, and 24 hours after PXO61 or mock inoculation from Rb49 and MDJ8. Leaf fragments approximately 2 cm in length that were immediately next to the inoculation site were collected.

2016-02-25 | E-GEOD-69242 | biostudies-arrayexpress

RNA-seq data of four Lupinus angustifolius lines profiled for anthracnose resistance, based on leaves RNA isolates from inoculated and control (mock-inoculated) plants

Project description:Resistant lines (Mandelup, carrying the AnMan allele and 83A:476 carrying the Lanr1 allele), the line which is putative novel donor of resistance (Boregine) and a susceptible line (Population 22660) were used in this study. 4 weeks after sowing, when the plants reached 4-6 leaf stage, plants were inoculated with Colletotrichum lupini or mock-inoculated (control plants) and then kept for 24 hours in darkness under ~100% humidity and temperature of 25°C. Leaves were sampled at 6, 12, 24, 36, and 48 hours post inoculation.

2022-11-02 | E-MTAB-11164 | 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

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

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