Resources of the Wageningen Seed Lab

On this page you will find some resources that are provided by the Wageningen Seed Lab.

The Germinator

Automatic scoring and curve fitting of Arabidopsis Germination:

Dormancy Gene Expression Plots

Gene expression data of dormant (D) and after-ripened (AR) Cvi seeds in temporal and spatial detail, D and AR NILDOG samples and Col-0 seed germination samples were combined. The expression profile of a gene of interest can be visualized across all these samples allowing quick determination of the behaviour of a gene of interest. Also indicated are genes whose expression patterns are highly correlated to the gene of interest (Dekkers, Pearce et al. manuscript in preparation).

Germination eFP brower

Gene expression visualisations of a high resolution time-course of germinating Arabidopsis seeds.
An Electronic Fluorescent Pictograph (eFP) browser (Winter et al., 2007) visualizes gene expression of seed germination, analysing expression in separated radicle+hypocotyl, cotyledons, micropylar and peripheral endosperm (Dekkers, Pearce et al. Plant Physiology 2013).

Based on the high resolution dataset of germinating Arabidopsis seeds two gene co-expression networks were created, one for micropylar endosperm samples (EndoNet) and one for the radicle+hypocotyl samples (RadNet).

EndoNet

A queryable interface of a genome-wide co-expression network model describing transcriptional interactions in the micropylar endosperm of germinating Arabidopsis seeds (Dekkers, Pearce et al. Plant Physiology 2013).

RadNet

A queryable interface of a genome-wide co-expression network model describing transcriptional interactions in the radicle+hypocotyl of germinating Arabidopsis seeds (Dekkers, Pearce et al. Plant Physiology 2013).

MapMan

Seed specific maps for MapMan as published in Joosen, R. V. L., W. Ligterink, et al. (2011). "Visualization of molecular processes associated with seed dormancy and germination using MapMan." Seed Science Research 1-10. For download please click on the "Map Man files" at the bottom of this page.

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