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| Status |
Public on Apr 24, 2008 |
| Title |
Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe) |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
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| Summary |
In order to estimate the effects of protoplasting and FACS sorting procedures on -Fe regulated gene expression we generated expression profiles for whole roots that had been treated with -Fe for 24 hours and for roots that were protoplasted and FACS sorted after the initial 24 hour -Fe treatment.
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: effects of protoplasting and FACS sorting
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| Overall design |
To estimate the effect that protoplasting and cell sorting has on the expression of -Fe regulated genes we prepared samples as in Birnbaum et al. (2005) Nat. Methods, except that all cells were collected after cell sorting. Cells were collected from roots that had been exposed to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no ferrous sulfate) for 24 hours prior to protoplasting. Whole roots were also collected after a similar treatment regimen with -Fe. Three replicates were performed per condition.
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| Contributor(s) |
Long TA, Wang JY, 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) |
tlong@duke.edu
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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 (6)
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| GSM265411 |
Arabidopsis, whole roots, -Fe, replicate 1 |
| GSM265412 |
Arabidopsis, whole roots, -Fe, replicate 2 |
| GSM265413 |
Arabidopsis, whole roots, -Fe, replicate 3 |
| GSM265414 |
Arabidopsis, root cells, -Fe, replicate 1 |
| GSM265415 |
Arabidopsis, root cells, -Fe, replicate 2 |
| GSM265416 |
Arabidopsis, root cells, -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 |
| BioProject |
PRJNA108927 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE10496_RAW.tar |
13.5 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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