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Series GSE10501 Query DataSets for GSE10501
Status Public on Apr 24, 2008
Title Expression analysis of root cell-types after iron deficiency (-Fe) treatment
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to -Fe media for 24 hours.
Little is known about how developmental cues affect the way cells interpret their environment. Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes. We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects. By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type.
Keywords: Cell-type specific analysis using FACS
Overall design To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of -Fe stress on gene expression along the radial axis of the root. Cell identity is the main variable that changes along the radial axis with the epidermis representing the outermost tissue layer and the stele representing the inner most layer. 5 different GFP reporter lines were used to isolate specific populations of cells from the Arabidopsis root using FACS sorting of protoplasted cells. GFP-reporter lines were exposed to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no ferrous sulfate) for 24 hours before hand.
Contributor(s) Long TA, Dinneny JR, Wang JY, Lee J, Benfey PN
Citation(s) 18436742
Submission date Feb 12, 2008
Last update date Aug 28, 2018
Contact name Terri Anita Long
Phone 919-613-8202
Fax 919-613-8177
Organization name Duke University
Department Biology
Lab Philip Benfey
Street address Box 90338
City Durham
State/province NC
ZIP/Postal code 27707
Country USA
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (16)
GSM266662 Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 1
GSM266663 Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 2
GSM266664 Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 3
This SubSeries is part of SuperSeries:
GSE10576 Iron deficiency (-Fe) effect: Arabidopsis roots
Affiliated with GSE69995
BioProject PRJNA108933

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
GSE10501_RAW.tar 54.2 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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