Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Maize coleoptilar node development: WT vs. rtcs      
dateReleased:
09-01-2013
description:
Maize (Zea mays L.) and other monocot cereals develop extensive shoot-borne root systems from nodal structures of the shoot to secure water and nutrient uptake and provide anchorage in the soil. In the present study, the early stages of coleoptilar node (first shoot-node) development of maize were subjected to a detailed morphological and histological analysis followed by a comprehensive microarray profiling via 105 k oligonucleotide microarrays. Expression profiling identified 1,179 microarray features corresponding to 974 unique transcripts which were differentially expressed between three stages of wild-type B73 coleoptilar node development within the first four days after the initiation of this structure. Significantly, all but one of these microarray features were preferentially expressed at day four compared to day zero of coleoptilar node formation. Moreover, comparative microarray profiling of wild-type versus mutant rtcs coleoptilar nodes which do not initiate shoot-borne roots revealed 958 microarray features corresponding to 828 unique transcripts that were expressed in a RTCS dependent fashion. Differential gene expression during wild-type coleoptilar node development and between wild-type and rtcs coleoptilar nodes was confirmed for a subset of 24 genes by qRT-PCR. In order to identify direct downstream targets of RTCS in silico promoter analyses revealed 191 differentially expressed genes that contained at least one LBD motif in a 1 kb promoter region upstream of the ATG start codon. For six promoter sequences containing LBD motives EMSA experiments demonstrated RTCS binding, hence supporting the notion that differentially accumulated genes containing LBD motifs are direct downstream targets of RTCS. The complex RTCS dependent regulation of coleoptilar node development and crown root formation was illustrated by a wide variety of cellular functions represented by the differentially accumulated genes and in particular by the differentially accumulated genes containing LBD promoter motifs. 24 samples in total: 3 developmental stages (0, 2, 4) * 2 genotypes (WT, rtcs) * 4 biological replicates
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-25467
refinement:
raw
alternateIdentifiers:
25467
keywords:
functional genomics
dateModified:
06-02-2014
availability:
available
types:
gene expression
ID:
A-GEOD-10837
name:
Maize Pioneer Hi-Bred 105K mRNA Microarray
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-25467/E-GEOD-25467.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-25467/E-GEOD-25467.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25467
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
Similar Datasets

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.