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| 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
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| 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
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| 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.
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| Contributor(s) |
Long TA, Dinneny JR, Wang JY, Lee J, Benfey PN |
| Citation(s) |
18436742 |
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| Submission date |
Feb 12, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Terri Anita Long |
| E-mail(s) |
[email protected]
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| Phone |
919-613-8202
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| Fax |
919-613-8177
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| Organization name |
Duke University
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| Department |
Biology
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| Lab |
Philip Benfey
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| Street address |
Box 90338
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27707 |
| Country |
USA |
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| Platforms (1) |
| GPL198 |
[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array |
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| Samples (16)
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| 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 |
| GSM266665 |
Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 4 |
| GSM266666 |
Arabidopsis, root cells, columella root cap, -Fe, replicate 1 |
| GSM266667 |
Arabidopsis, root cells, columella root cap, -Fe, replicate 2 |
| GSM266668 |
Arabidopsis, root cells, columella root cap, -Fe, replicate 3 |
| GSM266669 |
Arabidopsis, root cells, cortex, -Fe, replicate 1 |
| GSM266670 |
Arabidopsis, root cells, cortex, -Fe, replicate 2 |
| GSM266671 |
Arabidopsis, root cells, cortex, -Fe, replicate 3 |
| GSM266672 |
Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 1 |
| GSM266673 |
Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 2 |
| GSM266674 |
Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 3 |
| GSM266675 |
Arabidopsis, root cells, stele, -Fe, replicate 1 |
| GSM266676 |
Arabidopsis, root cells, stele, -Fe, replicate 2 |
| GSM266677 |
Arabidopsis, root cells, stele, -Fe, replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE10576 |
Iron deficiency (-Fe) effect: Arabidopsis roots |
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| Relations |
| Affiliated with |
GSE69995 |
| BioProject |
PRJNA108933 |
| 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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