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Series GSE34130 Query DataSets for GSE34130
Status Public on Sep 01, 2013
Title Ecotype specific nitrogen responses in the Arabidopsis root
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies.
We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.
 
Overall design The whole experiment was carried out in triplicate with 42 chips in total (14 experiments). The nitrogen response in seven Arabidopsis thaliana ecotype (Col0, Kas2, NFA8, SQ8, TAMM27, Ts5, Var2-1) whole roots was assayed using Affymetrix microarrays. Seedlings were grown hydroponically in low nitrogen for 12 days, then 5mM KNO3 was used as a nitrogen treatment for 2 hours with 5mM KCl used as a control treatment for the same length of time. At the end of the treatment time roots were harvested and flash-frozen in liquid nitrogen for subsequent RNA extraction.
For *Probe_Elements_Removed* file descriptions, please see the Sample records' "Data processing" annotations.
 
Contributor(s) Birnbaum KD, Coruzzi GM, Gifford ML, Katari MS
Citation(s) 24039603
Submission date Dec 04, 2011
Last update date May 14, 2020
Contact name Kenneth David Birnbaum
E-mail(s) ken.birnbaum@nyu.edu
Phone 212-998-8257
Organization name New York University
Department Biology
Lab Birnbaum
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10003
Country USA
 
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (42)
GSM842202 Col0 roots 2hr KCl control treated, biological rep1
GSM842203 Col0 roots 2hr KCl control treated, biological rep2
GSM842204 Col0 roots 2hr KCl control treated, biological rep3
Relations
Affiliated with GSE69995
BioProject PRJNA149857

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE34130_Kas2C_Probe_Elements_Removed.txt.gz 90.0 Kb (ftp)(http) TXT
GSE34130_Kas2T_Probe_Elements_Removed.txt.gz 71.7 Kb (ftp)(http) TXT
GSE34130_Key_For_Probe_Elements_Removed_RowNames.txt.gz 51.0 Kb (ftp)(http) TXT
GSE34130_NFA8C_Probe_Elements_Removed.txt.gz 79.9 Kb (ftp)(http) TXT
GSE34130_NFA8T_Probe_Elements_Removed.txt.gz 51.3 Kb (ftp)(http) TXT
GSE34130_RAW.tar 95.1 Mb (http)(custom) TAR (of CEL)
GSE34130_SQ8C_Probe_Elements_Removed.txt.gz 98.2 Kb (ftp)(http) TXT
GSE34130_SQ8T_Probe_Elements_Removed.txt.gz 88.8 Kb (ftp)(http) TXT
GSE34130_TAMM27C_Probe_Elements_Removed.txt.gz 79.2 Kb (ftp)(http) TXT
GSE34130_TAMM27T_Probe_Elements_Removed.txt.gz 80.1 Kb (ftp)(http) TXT
GSE34130_Ts5C_Probe_Elements_Removed.txt.gz 133.4 Kb (ftp)(http) TXT
GSE34130_Ts5T_Probe_Elements_Removed.txt.gz 107.0 Kb (ftp)(http) TXT
GSE34130_Var2-1C_Probe_Elements_Removed.txt.gz 59.9 Kb (ftp)(http) TXT
GSE34130_Var2-1T_Probe_Elements_Removed.txt.gz 58.5 Kb (ftp)(http) TXT
Processed data included within Sample table
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