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Series GSE10496 Query DataSets for GSE10496
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
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
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.
Contributor(s) Long TA, Wang JY, 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 (6)
GSM265411 Arabidopsis, whole roots, -Fe, replicate 1
GSM265412 Arabidopsis, whole roots, -Fe, replicate 2
GSM265413 Arabidopsis, whole roots, -Fe, replicate 3
This SubSeries is part of SuperSeries:
GSE10576 Iron deficiency (-Fe) effect: Arabidopsis roots
BioProject PRJNA108927

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
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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