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Arabidopsis thaliana
23 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Transcript profiling analysis of csn3-1, csn4-1 and csn5 (csn5a-2 csn5b) light grown and dark grown mutant seedlings compared to light grown and dark grown wild type using Arabidopsis ATH1 GeneChip array
Publication Title
The Arabidopsis COP9 signalosome is essential for G2 phase progression and genomic stability.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Analysis of gene expression in the meristematic zone of Arabidopsis roots overexpressing miR396
Publication Title
MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In order to identify candidate target genes of the OBP1 (At3g50410) transcription factor we used dexamethasone inducible system (Lloyd et al, 1994). A single inducible over-expression line was compared to an empty vector control line 10h after DEX induction to identify candidate genes that were confirmed by quantitative RT-PCR.
Publication Title
The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 17 Downloadable Samples
Illumina HiSeq 2000
Description
Wounding is a primary trigger of organ regeneration but how wound stress reactivates cell proliferation and promotes cellular reprogramming remains elusive. In this study we combined the transcriptome analysis with quantitative hormonal analysis to investigate how wounding induces callus formation in Arabidopsis thaliana. Our time-course RNA-seq analysis revealed that wounding induces dynamic transcriptional changes that can be categorized into five clusters with distinct temporal patterns. Gene ontology analyses uncovered that wounding modifies the expression of hormone biosynthesis and response genes, and quantitative analysis of endogenous plant hormones revealed accumulation of cytokinin prior to callus formation. Mutants defective in cytokinin synthesis and signalling display reduced efficiency in callus formation, indicating that de novo synthesis of cytokinin has major contribution in wound-induced callus formation. We further demonstrate that type-A ARABIDOPSIS RESPONSE REGULATOR (ARR)-mediated cytokinin signalling regulates the expression of CYCLIN D3;1 (CYCD3;1) and mutations in CYCD3;1 and its homologs CYCD3;2-3 cause defects in callus formation. Our transcriptome data, in addition, showed that wounding activates multiple developmental regulators, and we found novel roles of ETHYLENE RESPONSE FACTOR 115 (ERF115) and PLETHORA3 (PLT3), PLT5, PLT7 in wound-induced callus formation. Together, this study provides novel mechanistic insights into how wounding reactivates cell proliferation during callus formation. Overall design: Examination of transcriptome at 0, 1, 3, 6, 12,24 h after wounding.
Publication Title
Wounding Triggers Callus Formation via Dynamic Hormonal and Transcriptional Changes.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This experiment was set up in order to identify the (direct) transcriptional targets of the Ethylene Response Factor 115 (ERF115) transcription factor. Because ERF115 expression occurs in quiescent center (QC) cells and strong effects on the QC cells were observed in ERF115 overexpression plants, root tips were harvested for transcript profiling in order to focus on root meristem and QC specific transcriptional targets.
Publication Title
ERF115 controls root quiescent center cell division and stem cell replenishment.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Endocycle is an alternative cell cycle during which the DNA is replicated in the absence of cytokinesis, resulting in cellular endopolyploidy. The endocycle is frequenctly observed in plant species that grow under extreme conditions. Thus, endopolyploidy has been postulated to be a mechanism facilitating adaptive growth.
Publication Title
A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 5 Downloadable Samples
- NextSeq 500
Description
Somatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates, but is especially prominent in higher plants where it has been postulated to be essential for cell growth and fate maintenance. However, a comprehensive understanding of the physiological significance of plant endopolyploidy has remained elusive. Here, we modeled and experimentally verified a high-resolution DNA endoploidy map of the developing Arabidopsis thaliana root, revealing a remarkable spatiotemporal control of DNA endoploidy levels across tissues and a strong dependence on stress signals. Cellular and transcriptomic analysis revealed that inhibition of endoreplication onset alters the nuclear-to-cellular volume ratio and change in expression of cell wall modifying genes, correlated with the appearance of cell structural changes. Our data indicate that endopolyploidy might serve to coordinate cell expansion with structural stability, and that spatiotemporal endoreplication pattern changes may buffer for stress conditions, which may explain the widespread occurrence of the endocycle in plant species growing in extreme or variable environments. Overall design: Two biological replicates of Col-0 were compared with three biological replicates of smr1
Publication Title
A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation.
Sample Metadata Fields
Specimen part, Subject
View Samples- Arabidopsis thaliana
- 30 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis seedlings, of both wild-type and an ARF7/ARF19 double knockout mutant, were grown to 7 days post-germination. The roots were then dissected into 5 developmental zones, the meristem, early elongation zone, late elongation zone, mature root and lateral root zone. The sections then underwent transcriptional profiling to identify processes and regulatory events specific and in common to the zones.
Publication Title
A novel aux/IAA28 signaling cascade activates GATA23-dependent specification of lateral root founder cell identity.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 115 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background: The prognostic value of histologic grade (HG) in invasive lobular carcinoma (ILC) remains uncertain, and most ILC tumors are graded as HG2. Genomic grade (GG) is a 97-gene signature that improves the prognostic value of HG. This study evaluates whether GG may overcome the limitations of HG in ILC.
Publication Title
Genomic grade adds prognostic value in invasive lobular carcinoma.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage
View Samples
GSE36769- Homo sapiens
- 58 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
CD4⁺ follicular helper T cell infiltration predicts breast cancer survival.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Treatment
View Samples