Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 12
Release date: Dec 7 2006
Last update date: Dec 6 2012
Access: Public
Chemicals: Quaternary Ammonium Compounds, Aspartic Acid, Carbon, Chlorophyll, Nitrates, Nitrogen, Glutamic Acid
Dataset link Dissecting the rice genes responsible for long time changes of nitrogen supply forms and nitrogen starvation

Experimental Protocol


Rice seedlings were grown in a hydroponic system in a growth chamber with control of both temperature and light. After normal growth for two weeks and for one week with completely avoiding any N source, the plants at four and a half leaf stage were re-supplied with ammonium nitrate (equal amount of either form of N), or only ammonium (ammonium sulphate and ammonium chloride), or only nitrate (calcium nitrate and magnesium nitrate), and continuing at zero N (N starvation). All the other essential nutrients were the same for all four treatments, except for sulfate and chloride which ranged between 1.1 – 2.6 mM and 0.5 – 2.5 mM, respectively. In Arabidopsis, addition of 3 mM Cl to ‘controls’ did not produce any changes in the expression of genes in an experiment investigating the re-supply of 3 mM nitrate (Scheible et al., 2004). In other microarray experiments, extra addition of 5 mM Cl for Arabidopsis (Wang et al., 2000; Wang et al., 2004) and 1.4 mM sulphate for tomato (Wang et al., 2001) were used to replace nitrate for identifying the N deprivation responsive genes. Therefore, we assume that the relative smaller difference in sulfate and chloride concentrations among the four treatments in the normal supply range for plants would not significantly affect the expression profile of genes responsible for changes in N supply form and starvation in our experiments. For identifying the genes responding to the various N conditions by micro-array analysis, we extracted total RNA respectively from the roots and shoots at the 96 h after initiation of the four respective treatments. We used amplified and labeled cRNA from ammonium nitrate treatment as control, we performed array-hybridization for the cRNA from the treatment of single ammonium form, single nitrate form, or continuous N depletion, respectively. Agilent 60-mer oligonucleotide arrays containing 21,938 unique transcription units (Agilent Technologies, Tokyo, Japan) were used. Two biological replicates of each treatment were performed for microarray analyses.

Repositories


GEO

GSE4409

ArrayExpress

E-GEOD-4409

BioProject

PRJNA94639

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Contact


Guohua Xu