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High resolution NO3 response of Arabidopsis Roots
Gabriel Krouk, New York University, Center for Genomics and Systems Biology, New York, New York (gloria.coruzzi@nyu.edu)
Experiment design (26 hybridizations)
time
•0 mins •3 mins •6 mins •9 mins •12 mins •15 mins •20 mins
compound
•Basal medium •KCl •KNO3

This experiment has been imported by PLEXdb from NCBI GEO (GSE20044) Series_summary: This work uses a time series in order to decipher gene re...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: High resolution NO3 response of Arabidopsis Roots
Accession No: AT108
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
time
•0 mins  •3 mins  •6 mins  •9 mins  •12 mins  •15 mins  •20 mins
compound
•Basal medium   •KCl   •KNO3
Quality Control: biological replicates
Treatment summary:
 time  compound  # replicates
 0 mins  Basal medium  2
 0 mins  KCl  0
 0 mins  KNO3  0
 3 mins  Basal medium  0
 3 mins  KCl  2
 3 mins  KNO3  2
 6 mins  Basal medium  0
 6 mins  KCl  2
 6 mins  KNO3  2
 9 mins  Basal medium  0
 9 mins  KCl  2
 9 mins  KNO3  2
 12 mins  Basal medium  0
 12 mins  KCl  2
 12 mins  KNO3  2
 15 mins  Basal medium  0
 15 mins  KCl  2
 15 mins  KNO3  2
 20 mins  Basal medium  0
 20 mins  KCl  2
 20 mins  KNO3  2
Total hybridizations: 26
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE20044)

Series_summary:
This work uses a time series in order to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to NO3- provision. The experimental approach has been to monitor genome response to NO3- at 3, 6, 9, 12, 15 and 20 min, using ATH1 chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by very fast (within 3 min) gene expression modulation, involving genes/functions needed to prepare plants to use/reduce NO3-. State-space modeling (a machine learning approach) has been used to successfully predict gene behavior in unlearnt conditions.

Series_overall_design:
26 Samples: 2 at time 0 with no treatment; 4 at time 3, 2 with KCL and 2 with KNO3 treatment; 4 at time 6, 2 with KCL and 2 with KNO3 treatment; 4 at time 9, 2 with KCL and 2 with KNO3 treatment; 4 at time 12, 2 with KCL and 2 with KNO3 treatment; 4 at time 15, 2 with KCL and 2 with KNO3 treatment; 4 at time 20, 2 with KCL and 2 with KNO3 treatment;
Publication: 'Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate.', Krouk G, Mirowski P, Lecun Y, Shasha DE, Coruzzi GM.
Genome Biol 2010 Dec 23;11(12):R123.
pubmed: 21182762
Created: 2011-02-18 14:23:11
Last Update: 2011-02-18 15:01:38
Released: 2011-02-24
GEO Accession GSE20044
Submitter: PLEXdb Curator
Name: Gabriel Krouk
Institution: New York University, Center for Genomics and Systems Biology, New York, New York
Head of Laboratory: Gloria M Coruzzi
email(s):
Homepage:

 
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