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Series GSE9996 Query DataSets for GSE9996
Status Public on Oct 30, 2008
Title Organ regeneration in plants is independent of stem cell niche activity
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary A critical step in regeneration is recreating the cellular identities and patterns of lost organs long after embryogenesis is complete. In plants, perpetual (indeterminate) organ growth occurs in apical stem cell niches, which have been shown to re-establish quickly when damaged or removed (1,2). Here we ask whether the machinery of perpetual organ growth, stem cell activity, is needed for the phase of regeneration that leads to replenishing lost cell identities and patterning, or, whether organ re-establishment enlists a wider group of pluripotent cells. We adapt a root tip regeneration system to Arabidopsis that permits us to assess the molecular and functional recovery of specific cell fates during organ regeneration. These results suggest a rapid restoration of missing cell fate and function in advance of the recovery of stem cell activity. Surprisingly, plants with mutations that fail to maintain stem cell activity were able to re-pattern their distal tip and re-specify lost cell fates. Thus, although stem cell activity is required to resume indeterminate growth (3), our results show it is not necessary for cell re-specification and patterning steps. This implies a regeneration mechanism that coordinates patterning of the whole organ, as in embryogenesis, but is initiated from different starting morphologies. 1. Feldman, L. J. Denovo Origin of Quiescent Center Regenerating Root Apices of Zea-Mays. Planta 128, 207-212 (1976). 2. Xu, J. et al. A molecular framework for plant regeneration. Science 311, 385-8 (2006). 3. Gordon, S. P. et al. Pattern formation during de novo assembly of the Arabidopsis shoot meristem. Development 134, 3539-48 (2007).
We adapted root tip excision techniques to Arabidopsis, enabling us to perform microarray profiling of regenerating root tissue. Excisions were performed at 4 days post-germination (dpg) at a distance of 130 um from the root tip, resulting in the complete excision of QC, all surrounding stem cells along with several tiers of daughter cells, and the root cap, including all of the columella and most of the lateral root cap. The tip section and then approximately 70 um of regenerating tissue was recut at different time points post cutting. We sampled regenerating stumps at 0hrs, 5 hrs, 13 hrs, 22 hrs, and 7 days after the excision for microarray analysis (Methods). We also sampled root sections immediately above the zone competent to regenerate at 270 um to approximately 340 um.
Keywords: time course, development, root regeneration
Overall design 30 samples with 4 or 3 replicates for each condition representing a time course of regenerating root stumps and including controls for root tips (regeneration endpoint) at 4 dpg and 8 dpg and a wounded set of samples representing root tissue at 270-340 mm from the root tip for non-regeneration control
Contributor(s) Birnbaum KD, Sena G, Wang X, Liu H
Citation(s) 19182776
Submission date Dec 20, 2007
Last update date Aug 28, 2018
Contact name Kenneth David Birnbaum
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 (30)
GSM252663 Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep1
GSM252664 Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep2
GSM252665 Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep3
Affiliated with GSE69995
BioProject PRJNA104017

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Supplementary file Size Download File type/resource
GSE9996_RAW.tar 67.3 Mb (http)(custom) TAR (of CEL, EXP)
Raw data provided as supplementary file
Processed data included within Sample table

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