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GSE34004
Arabidopsis thaliana
18 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Background: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes the first genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation. Results: Genome-wide profiling revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified novel cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of primary versus redundant members of closely related gene families with respect to phosphate-starvation. Thus, among others, we show that PHO1 acts in shoot, whereas PHO1;H1 is likely the primary regulator in root. Conclusion: Our results uncover a much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the highest resolution of genome-wide data on plant nutrient stress to date.
Publication Title
The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The functions of miRNAs and their target mRNAs in Arabidopsis development have been widely documented, however, roles of stress responsive miRNAs and their targets are not as well understood. Using small RNA deep sequencing and ATH1 microarrays to profile mRNAs, we identified IAR3 (IAA-Ala Resistant 3) as a novel target of miR167a.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Zea mays
- 12 Downloadable Samples
Illumina HiSeq 2000
Description
The research of maize freezing tolerance.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare
- 156 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
We measured mRNA abundance in the embryogenic tissue of 150 recombinant Steptoe x Morex doubled-haploid lines (no replicates) and in parental genotypes, Steptoe and Morex, 3 replicates each, total 156 chips.
Publication Title
SFP genotyping from affymetrix arrays is robust but largely detects cis-acting expression regulators.
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Hordeum vulgare
- 24 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
We measured mRNA abundance in the seedling leaves of 8 barley genotypes; Morex, Steptoe, Golden Promise, Optic, Haruna Nijo, Barke, OWB-D and OWB-R. 3 biological replicates each, total 24 chips.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Zea mays
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-seq data of maize three root types (primary, seminal and crown roots)early in development
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part, Disease, Treatment
View Samples- Zea mays
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
This study analyzed the regulation of polyaspartic acid on the nitrate response of maize at transcriptional level.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Treatment
View Samples- Zea mays
- 8 Downloadable Samples
- Illumina Genome Analyzer II
Description
In this study the transcriptomes of 2cm-long primary roots (without apical 5mm) of wildtype and rum1 mutant seedlings were compared to identify genes directly or indirectly regulated by RUM1. Besides the RUM1-dependent gene network, novel functions of RUM1 were revealed.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Disease, Treatment
View Samples- Zea mays
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
In this study RNA-sequencing was used to monitor gene expression changes in stele tissue of maize (Zea mays L.) shoot-borne roots in response to local high nitrate stimulation to gain a better understanding of the mechanisms underlying nitrate signal and lateral root development.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part, Disease, Treatment
View Samples