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Browse PoplarPLEX Experiment Data

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Transcriptome profiling data for secondary vascular tissue regeneration in Populus tomentosa
Jing Zhang, Peking University, College of Life Sciences, Beijing, China (zhangj06@gmail.com)
Experiment design (10 hybridizations)
developmental stage name
•diX •deX •rPh •diC •rC

This experiment has been imported by PLEXdb from NCBI GEO (GSE25309)

Series_summary:
Regeneration is a common strategy for plants to ...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Transcriptome profiling data for secondary vascular tissue regeneration in Populus tomentosa
Accession No: PT46
Microarray: Poplar61k
Visibility: public
Experiment Type:
Experiment Factor(s):
developmental stage name
•diX   •deX   •rPh   •diC   •rC
Quality Control: biological replicates
Treatment summary:
 developmental stage name  # replicates
 diX  2
 deX  2
 rPh  2
 diC  2
 rC  2
Total hybridizations: 10
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE25309)

Series_summary:
Regeneration is a common strategy for plants to repair their damaged body plans after attack from other organisms or physical assaults. Trees with bark girdling on a large scale will grow new bark within one month and this bark regeneration after girdling system has been proven to be an efficient method to study secondary vascular development as well as plant tissue regeneration in vivo.
We herein show the molecular features of differentiating xylem cell fate switch process during secondary vascular tissue (SVT) regeneration in Populus. Based on our data, we propose a working model to illustrate the molecular dynamics underlying xylem cell fate switch process during SVT regeneration, which is significant to understand the pattern formation during the SVTs regeneration and also would shed light on the mechanisms of tissue regeneration in plants.

Series_overall_design:
Specific regenerated tissues of Populus at different stages were isolated by tangential cryo-sectioning. Total RNA from cryo-sections representing different regenerating tissues was extracted for Affymetrix Poplar Whole Genome Array hybridization. Five samples (two replicates for each sample) were used for gene expression analysis: differentiating xylem (diX, Stage 0), dedifferentiating xylem cells (deX, Stage I), regenerated phloem (rPh, Stage II), differentiating regenerated cambium (diC, Stage II) and regenerated cambium (rC, Stage III). In addition, one pooled genomic DNA sample from cryo-sections of differentiating xylem from two trees was isolated for DNA hybridization to produce a new CDF file that was used to mask out some potentially cross-hybridizing probesets from the standard Affymetrix Poplar Genome Array.
Supplementary file: poplar.cdf

PLEXdb Curator Notes:
Key for GEO Samples:
diX-differentiating xylem
deX-dedifferentiating xylem cells
rPh-regenerated phloem
diC-differentiating regenerated cambium
rC-regenerated cambium

We have not included the sample labelled 'diX for DNA extraction' because it has not been used for gene expression measurements.
Publication: 'Molecular features of secondary vascular tissue regeneration after bark girdling in Populus.', Zhang J, Gao G, Chen JJ, Taylor G, Cui KM, He XQ.
New Phytol 2011 Dec;192(4):869-84.
pubmed: 21883236
Created: 2012-08-29 14:57:18
Last Update: 2012-09-10 14:26:24
Released: 2012-09-10
GEO Accession GSE25309
Submitter: PLEXdb Curator
Name: Jing Zhang
Institution: Peking University, College of Life Sciences, Beijing, China
Head of Laboratory: --
email(s):
Homepage:

 
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