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GSE30223
Arabidopsis thaliana
28 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In depth temporal profiling of transcript changes at 10 time points during germination in Arabidopsis seed was carried out. The time course utilised, encompassed seed maturation, stratification, germination and post-germination and provided a global investigation into the tightly regulated, phasic changes that define seed germination.
Publication Title
In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis.
Sample Metadata Fields
Specimen part, Disease, Time
View Samples- Oryza sativa
- 24 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
In response to bacterial infection, early transcriptional re-programming occurs in the host plant.
Publication Title
Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 29 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In response to WRKY40 and WRKY60 perturbation (and high light stress), significant transcriptional re-programming occurs particularly for genes encoding stress responsive mitochondrial and choloplast proteins.
Publication Title
AtWRKY40 and AtWRKY63 modulate the expression of stress-responsive nuclear genes encoding mitochondrial and chloroplast proteins.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Oryza sativa
- 15 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Transcript abundance profiles were examined over the first 24 hours of germination in rice grown under aerobic conditions.
Publication Title
Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity.
Sample Metadata Fields
Specimen part, Time
View Samples- Populus tremula x populus alba
- 29 Downloadable Samples
- Affymetrix Poplar Genome Array (poplar)
Description
The molecular responses of Grey poplar (Populus x canescens) following root hypoxia were studied in roots and leaves using transcript profiling. Grey poplar is a flooding tolerant tree species and analysis of the molecular response to hypoxia may indicate possible adaptation mechanisms to this stress.
Publication Title
Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia.
Sample Metadata Fields
No sample metadata fields
View Samples- Oryza sativa
- 11 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
The antagonistic interaction between iron (Fe) and phosphorus (P) has been noted in the area of plant nutrition. To understand the physiology and molecular mechanisms of this interaction, we studied the growth performance, nutrient concentration, and gene expression profiles of root and shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under four different nutrient conditions: (1) full strength of Fe and P (+Fe+P); (2) full strength of P and no Fe (-Fe+P); (3) full strength of Fe and no P (+Fe-P); and (4) without both Fe and P (-Fe-P).
Publication Title
Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 9 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Analysis of changes in global transcript abundance profiles of 2 week old tim23 OE (overexpressor) and tim23 KO (knock-out) mutant Arabidopsis plants complared to wild-type (Col-0) using Affymetrix GeneChipﾙ Arabidopsis ATH1 Genome Arrays.
Publication Title
Dual location of the mitochondrial preprotein transporters B14.7 and Tim23-2 in complex I and the TIM17:23 complex in Arabidopsis links mitochondrial activity and biogenesis.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 29 Downloadable Samples
Illumina HiSeq 1000
Description
RNAseq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination. Overall design: Total RNA was extracted from Arabidopsis seeds at 10 time points during germination in triplicate. The time points were: freshly harvested seed (H), seeds following 15 days of ripening (0 h), seeds after; 1 h of stratification (1 h S), 12 h of stratification (12 h S), 48 h of stratification (48 h S), followed by seed collected 1 hour into the light (1 h SL), 6 hours into the light (6 h SL), 12 hours into the light (12 h SL), 24 hours into the light (24 h SL) and 48 hours into the light (48 h SL).
Publication Title
Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Defects in mitochondrial oxidative phosphorylation complexes, altered bioenergetics and metabolic shift are often seen in cancers. Here we show a role for the dysfunction of electron transport chain component, cytochrome c oxidase (CcO) in cancer progression. We show that genetic silencing of the CcO complex by shRNA expression and loss of CcO activity in multiple cell types from the mouse and human sources resulted in metabolic shift to glycolysis, loss of anchorage dependent growth and acquired invasive phenotypes. Disruption of CcO complex caused loss of transmembrane potential and induction of Ca2+/Calcineurin-mediated retrograde signaling. Propagation of this signaling, includes activation of PI3-kinase, IGF1R and Akt, Ca2+ sensitive transcription factors and also, TGF1, MMP16, periostin that are involved in oncogenic progression. Whole genome expression analysis showed up regulation of genes involved in cell signaling, extracellular matrix interactions, cell morphogenesis, cell motility and migration. The transcription profiles reveal extensive similarity to retrograde signaling initiated by partial mtDNA depletion, though distinct differences are observed in signaling induced by CcO dysfunction. The possible CcO dysfunction as a biomarker for cancer progression was supported by data showing that esophageal tumors from human patients show reduced CcO subunits IVi1 and Vb in regions that were previously shown to be hypoxic core of the tumors. Our results show that mitochondrial electron transport chain defect initiates a retrograde signaling. These results suggest that a defect in CcO complex can potentially induce tumor progression.
Publication Title
Disruption of cytochrome c oxidase function induces the Warburg effect and metabolic reprogramming.
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 3 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8<br></br>Comparison of transcript profiles between wild type Columbia and ccr1 (carotenoid and chloroplast regulatory) mutant, which contains a mutation in At1g77300 (SDG8)
Publication Title
Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8.
Sample Metadata Fields
Age
View Samples