Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

66 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Determination of genes expressed in response to drought in root and shoot of Leucaena leucocephala

ABSTRACT: Leucaena leucocephala seedlings were treated with PEG6000 and the shoot and root tissues were collected after 48 hours following the treatment. The gene expressions were compared between treated and untreated in root and shoot separately. The differentially expressed genes may be related to drought resistance. RNA from shoot and root from treated and untreated L. leucocephala seedlings were extracted. Two biological replicates were made for each sample (each replicate represents about 10 individual seedlings).

ORGANISM(S): Leucaena leucocephala

SUBMITTER: Kazue Ishihara

PROVIDER: E-GEOD-76810 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression analysis of Acacia koa in response to mechanical stimuli

Project description:The genes induced by mechanical stimuli may be also involved in disease resistance and wood formation and development in Acacia koa. If so, mechanically stressed A. koa may be used as a model to study disease resistance and wood formation and development. Microarray analysis was performed to determine expression levels of 4,000 genes related to disease resistance and wood development in Acacia koa in response to mechanical stimuli (touch). RNA was extracted from two groups of A. koa seedlings, (1) mechanically stressed and (2) unstressed koa seedlings. Each group had two biological replicates (n=2), where n represents pools of approcimately 20 individuals.

2015-12-14 | E-GEOD-73889 | biostudies-arrayexpress

eQTL Mapping of the Drosophila Female Head Transcriptome

Project description:A dataset of ~600 RIL crosses using RILs from the Drosophila Synthetic Population Resource to be used for genomewide eQTL mapping. All samples are from female heads. 54 arrays with 12 samples per array resulting in data for 596 RIL crosses.

2013-11-06 | E-GEOD-52076 | biostudies-arrayexpress

Transcriptome analysis of Enterococcus faecalis OG1 delta-EF2638 mutant

Project description:Analysis of changes in gene expression in Enterococcus faecalis OG1 delta-EF2638 mutant compared to wild-type OG1 strain. The deletion mutant has a growth defect when grown with aeration The mutant presented in this study is described and characterized in Vesic, D. and Kristich, C.J. 2012. A Rex-family transcriptional repressor influnces H2O2 accumulation by Enterococcus faecalis. (submitted for publication) Microarray analysis was done using RNA isolated from two independent cultures of wild-type Enterococcus faecalis OG1 and two independent cultres of Enterococcus faecalis OG1 delta-EF2638 mutant; each RNA sample was subjected to triplicate hybridization (technical replicates) . Microarrays were custom designed to investigate expression of ORFs in Enterococcus faecalis OG1RF genome. The arrays were designed based on the OG1RF annotation generated with the Rapid Annotation Using Subsystem Technology (RAST) server (Aziz et. al. 2008. BMC Genomics 9:75), as described in Frank et al (2012) Infect. Immun. 80:539. The aim was eighteen probe pairs per ORF, each of which is present in triplicate.

2013-04-15 | E-GEOD-43228 | biostudies-arrayexpress

Unraveling epigenetic changes in A. thaliana calli: Impact of HDAC inhibitors

Project description:The aim was to characterize epigenetic changes in histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings using mass spectrometry-based approach. Increased level of histone H3.3 variant was found to be the most prominent feature of 20-day-old calli, associated with chromatin relaxation. Methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate and trichostatin A, although each HDACi affected the state of post-translational histone modifications in a specific manner.

2024-01-26 | PXD046788 | Pride

Transcriptome Analysis of Wounding-Induced Root to Shoot Communication in Arabidopsis thaliana.

Project description:Comparison of gene expression between shoots of root-wounded seedlings and shoots of control seedlings in Arabidopsis. We identified wounding-induced early (30 min) and late (360 min) root to shoot responsive genes (RtS). Two-condition experiment, shoots of root-wounded seedlings vs. shoots of control seedlings. Biological replicates: 2 control replicates, 2 treated replicates. Technical replicate: Dyeswap

2010-12-31 | E-GEOD-26374 | biostudies-arrayexpress

Phosphoproteomics of CEP5 peptide treatment Arabidopsis

Project description:While CEP5 has been shown to play a role in shoot and root growth, possibly through interaction with the CEPR1/XIP1 and/or CEPR2 receptor kinase, very little is known about the downstream molecular effects. To gain insight in the changes downstream of CEP5, we quantified differences in phosphoproteomes of peptide treatment seedlings using label-free mass spectrometry-based proteomics

2020-05-15 | PXD017444 | Pride

Expression analysis of shoots in Olea europaea cultivar M-bM-^@M-^XArbequinaM-bM-^@M-^Y collected at different growth time

Project description:Genetic changes involved in the juvenile-to-adult transition in the shoot apex of Olea europaea L. occurs years before the first flowering. For the study of the genetic-expression pattern over development, 21 seedlings originating from open pollination of olive cultivar M-bM-^@M-^XArbequinaM-bM-^@M-^Y were grown in a greenhouse in Centro IFAPA M-bM-^@M-^\ChurrianaM-bM-^@M-^] MM-CM-!laga, Spain. At the sixth month the apical shoot was removed and kept for genomic analysis. Any lateral shoot was removed to force the growth along just one axis. Every three months a new (1 cm long) apical-shoot tip was taken, which included the meristem down to two very small young leaves. When the apical-shoot tip is removed the two lateral buds immediately below are activated, one of them is removed, and the other one becomes the new apical-shoot tip. Seedlings reaching 50 nodes or 1 m high were allowed to form a top canopy. From then, the samples were taken from apical shoots of higher branches. We analyzed samples taken from the seedling/tree No 11, in a dense time-course study by microarray analysis. According to the nature of the samples, i.e. the main apical shoots, we had to use single samples during the first 6 to 15 months of growth. This limits the use of the statistics for this period but is compensated for by providing a series of consecutive data that make it possible to ascertain the time course of gene expression over plant development.

2013-11-09 | E-GEOD-52213 | biostudies-arrayexpress

Expression data from WT, MPK6 Overexpression, and mpk6 T-DNA knockout Arabidopsis root and shoot under hypoxic and mock conditions

Project description:MPK6 shows transient increase in activity under hypoxia with maximal activity at 2 hrs. To study the role of MPK6 in hypoxia in Arabidopsis, 10 do seedlings of WT, mpk6 and MPK6 plants were exposed to 2 hrs hypoxia and 2hr air (mock). Because there are no major phenotypic differences between the genotypes, microarray was used to determine if there were transcript level differences between the genotypes. Wild type Col-0, MPK6 overexpression and mpk6 knockout mutants were exposed to 2 hr hypoxia and air and separated into root and shoot in order to determine the role of MPK6 in hypoxia in both root and shoot.

2011-12-03 | E-GEOD-31158 | biostudies-arrayexpress

Transcriptome Analysis of Wounding-Induced Root to Shoot Communication in Arabidopsis thaliana.

2010-12-31 | GSE26374 | GEO

Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize

Project description:Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize We report an integrated genome-wide analysis of DNA methylation, histone modifications, smRNAs and mRNA transcriptional activity, using maize as a model. We surveyed the epigenomes of the maize inbred line B73 in shoot and root tissue by Illumina/Solexa 1G parallel sequencing after digesting genomic DNA with a methylation-sensitive restriction enzyme and after conducting chromatin immunoprecipitations (ChIP) using antibodies that target specific histone modifications (H3K4me3, H3K9ac, H3K27me3, H3K36me3, respectively). Additionally, we profiled RNA pools (micro RNA (miRNA), siRNA and mRNA) using the same sequencing strategy. Keywords: Epigenetics, mRNA transcription and small RNAs H3K4me3, H3K9ac, H3K27me3, H3K36me3, DNA methylation and mRNA, small RNA profiled from shoots and roots of 14 day-old maize B73 seedlings

2009-04-27 | E-GEOD-15286 | 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