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Series GSE7631 Query DataSets for GSE7631
Status Public on Dec 19, 2007
Title Cell-specific nitrogen responses in the Arabidopsis root
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary The organs of multicellular species are comprised of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change but little is known about how responses are tailored to specific cell types or coordinated among them on a global level. Here we use cellular profiling of five Arabidopsis root cell types in response to a limiting resource, nitrogen, to uncover a vast and predominantly cell-specific response that was largely undetectable using traditional methods. These methods reveal a new class of cell-specific nitrogen responses. As a proof-of-principle, we dissected one cell-specific response circuit that mediates nitrogen-induced changes in root branching from pericycle cells. Thus, cellular response profiling links gene modules to discrete functions in specific cell types.
Keywords: cell type comparison, comparative genomic hybridization, genetic modification
 
Overall design The whole experiment was carried out in triplicate with 84 chips in total (28 experiments). The nitrogen response in 5 FACS-sorted root cell types (LRC, lateral root cap; EpiC, epidermis and cortex; EndoP, endodermis and pericycle; Peri, pericycle; Stele, stele), protoplasts and Col-0 whole roots was assayed using microarrays. 5mM KNO3 was used as a nitrogen treatment for 2 hours. 5mM KCl was used as a control treatment for the same length of time. 1mM MSX in combination with 5mM KNO3 (or with 5mM KCl as a control) was used to block the assimilation of KNO3, and 5mM Gln added to restore it in order to seperate KNO3 effects from assimilated-nitrogen effects. 5mM KNO3 was either maintained in the protoplast-generating solution (continuous treat) or not (transitory treat) to test how to best preserve the cellular nitrogen-response during the 1 hr protoplast generating procedure. As controls we used protoplasts, whole roots frozen directly after the 2hr treatment or 3.5hr treatment, or whole roots incubated in protoplast-generating solution (minus enzymes; transitory or continuous treated) and then frozen. After FACS-sorting or mock FACS-sorting cells were frozen.
 
Contributor(s) Birnbaum KD, Coruzzi GM, Gifford ML, Dean A, Gutierrez RA
Citation(s) 18180456
Submission date Apr 26, 2007
Last update date Aug 28, 2018
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 (84)
GSM184476 Lateral Root Cap root cells 2hr KCl control treated, biological rep1
GSM184477 Lateral Root Cap root cells 2hr KCl control treated, biological rep2
GSM184478 Lateral Root Cap root cells 2hr KCl control treated, biological rep3
Relations
Affiliated with GSE69995
BioProject PRJNA100137

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
GSE7631_RAW.tar 163.4 Mb (http)(custom) TAR (of CEL, EXP)
Processed data included within Sample table
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