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GSE21876
Arabidopsis thaliana
12 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We isolated the meristematic and elongation zones of Col-0, upb1-1 mutant and 35S::UPB1-3YFP/upb1-1 plants by micro-dissection and extracted RNA from each section independently.
Publication Title
Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 10 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Transcriptional profile of whole roots of wild-type and pye-1 mutants exposed to 24 hours -Fe were generated
Publication Title
The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Understanding how the expression of transcription factor (TF) genes is modulated is essential for reconstructing gene regulatory networks. There is increasing evidence that sequences other than upstream noncoding can contribute to modulating gene expression, but how frequently they do so remains unclear. Here, we investigated the regulation of TFs expressed in a tissue-enriched manner in Arabidopsis roots. For 61 TFs, we created GFP reporter constructs driven by each TF's upstream noncoding sequence (including the 5'UTR) fused to the GFP reporter gene alone or together with the TF's coding sequence. We compared the visually detectable GFP patterns with endogenous mRNA expression patterns, as defined by a genome-wide microarray root expression map.
Publication Title
Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Pericycle specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) of roots that express a pericycle-specific GFP-reporter. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transferred to -Fe media for 24 hours.
Publication Title
The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 78 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 39 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The Oscillation Zone (OZ) of unsynchronized roots was disected and divided into an upper (OZ2) and lower (OZ1) half .
Publication Title
Oscillating gene expression determines competence for periodic Arabidopsis root branching.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 25 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
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 used. FACS cell populations were isolated from roots grown under standard pH (pH 5.7) or roots that had been transfered to low pH (pH 4.6) media for 24 hours.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
Illumina HiSeq 2500
Description
In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem (RAM), a group of slowly dividing quiescent center (QC) cells is thought to limit stem cell activity to directly neighboring cells (Cowels, 1956; van den Berg et al., 1997), thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction with the more gradual changes in cell division potential (Bennett and Scheres, 2010) and differentiation (Yamaguchi et al., 2008; 2010; Furuta et al, 2014; Geldner, 2013; Masucci et al., 1996; Dolan and Costa, 2001) that occur as cells move further away from the QC. To address this paradox and to infer molecular organization of the root meristem, we used a whole-genome approach to determine dominant transcriptional patterns along root ontogeny zones. We found that the prevalent patterns are expressed in two opposing gradients. One is characterized by genes associated with development, the other enriched in differentiation genes. We confirmed these transcript gradients, and demonstrate that these translate to gradients in protein accumulation and gradual changes in cellular properties. We also show that gradients are genetically controlled through multiple pathways. Based on these findings, we propose that cells in the Arabidopsis root meristem gradually transition from 'stemness' towards differentiation. Overall design: This study contains high-resolution datasets from cell populations from the enitre root meristem and xylem-specific cell populations. Using fluorescence activated cell sorting, three cell populations were isolated based on their GFP expression intensity. Two-Three replicates were used per sample
Publication Title
Framework for gradual progression of cell ontogeny in the <i>Arabidopsis</i> root meristem.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the effect of low pH on developmental stages in the root, we dissected the root into four developmental zones after exposure to low pH and expression profiled each zone.
Publication Title
Cell identity regulators link development and stress responses in the Arabidopsis root.
Sample Metadata Fields
Age
View Samples