Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 20
Release date: Oct 21 2011
Last update date: Mar 21 2012
Access: Public
Chemicals: Ozone
Dataset link Sun and shade leaves_2x ambient ozone_050805

Experimental Protocol


The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009). Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation. For one time point we had five microarrays and five dye-swaps for each of sun and shade leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.

Repositories


GEO

GSE17411

ArrayExpress

E-GEOD-17411

BioProject

PRJNA123407

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Contact


Maren Olbrich