Search   for 
Find Your Gene ·  Publications ·  Tools ·  Gene List Suite ·  Expression Atlases ·  About PLEXdb ·  Feedback
Login ID:
Pathogens & Symbionts
Search Experiments
Download Data
Gene List Suite
Your Account
 Data Release Policy 
PLEXdb is committed to making expression data publicly available to researchers world-wide...
complete policy

Browse TomPLEX Experiment Data

Choose an experiment:
Tomato root transcriptome response to a nitrogen-enriched soil patch
Dan Ruzicka, Donald Danforth Plant Science Center (,
Experiment design (9 hybridizations)
•water_control •low Nitrogen •high Nitrogen

This experiment has been imported by PLEXdb from NCBI GEO (GSE21020) Series_summary: Nitrogen (N), the primary limiting factor for plant growt...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Experiment Name: Tomato root transcriptome response to a nitrogen-enriched soil patch
Accession No: LE10
Microarray: tomato10k
Visibility: public
Experiment Type:
Experiment Factor(s):
•water_control   •low Nitrogen   •high Nitrogen
Quality Control: biological replicates
Treatment summary:
 nutrient  # replicates
 water_control  3
 low Nitrogen  3
 high Nitrogen  3
Total hybridizations: 9
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE21020)

Nitrogen (N), the primary limiting factor for plant growth and yield in agriculture, has a patchy distribution in soils due to fertilizer application or decomposing organic matter. Studies in solution culture over-simplify the complex soil environment where microbial competition and spatial and temporal heterogeneity challenge roots’ ability to acquire adequate amounts of nutrients required for plant growth. In this study, various ammonium treatments (as 15N) were applied to a discrete volume of soil containing tomato (Solanum lycopersicum) roots to simulate encounters with a localized enriched patch of soil. Transcriptome analysis was used to identify genes differentially expressed in roots 53 hrs after treatment. Results: The ammonium treatments resulted in significantly higher concentrations of both ammonium and nitrate in the patch soil. The plant roots and shoots exhibited increased levels of 15N over time, indicating a sustained response to the enriched environment. Root transcriptome analysis identified 585 genes differentially regulated 53 hrs after the treatments. Nitrogen metabolism and cell growth genes were induced by the high ammonium (65 ug NH4+-N g-1 soil), while stress response genes were repressed. The complex regulation of specific transporters following the ammonium pulse reflects a simultaneous and synergistic response to rapidly changing concentrations of both forms of inorganic N in the soil patch. Transcriptional analysis of the phosphate transporters demonstrates cross-talk between N and phosphate uptake pathways and suggests that roots increase phosphate uptake via the arbuscular mycorrhizal symbiosis in response to N. Conclusion: This work enhances our understanding of root function by providing a snapshot of the response of the tomato root transcriptome to a pulse of ammonium in a complex soil environment. This response includes an important role for the mycorrhizal symbiosis in the utilization of an N patch.

9 Total samples were analyzed across 3 treatment groups (3 biological replicates per group). We generated the following pairwise comparisons using JMP Genomics software: Control vs. Low N, Control vs. high N, and low N vs. high N. One way ANOVA was used to determine significantly different expression. Genes with an FDR≤10% were presented.
Publication: 'Tomato root transcriptome response to a nitrogen-enriched soil patch.', Ruzicka DR, Barrios-Masias FH, Hausmann NT, Jackson LE, Schachtman DP.
Plant Biol 2010 Apr 27;10:75.
pubmed: 20423508
Created: 2010-11-03 13:33:47
Last Update: 2010-11-03 13:47:47
Released: 2010-11-09
GEO Accession GSE21020
Submitter: PLEXdb Curator
Name: Dan Ruzicka
Institution: Donald Danforth Plant Science Center
Head of Laboratory: Daniel P Schachtman

Copyright@2001-2013 The PLEXdb Group
All rights reserved.

For problems with the webpages contact PLEXdb webmasters