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E-MEXP-301
Hordeum vulgare
5 Downloadable Samples
Affymetrix Barley Genome Array (barley1)
Description
Changes in gene expression during adaptation to abiotic stress conditions in the barley roots.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part, Time
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.
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
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Mus musculus
- 3 Downloadable Samples
Description
Current evidence suggests that more than half of the mammalian genome is transcribed, yet how this vast transcriptome is regulated in vivo remains poorly understood. We demonstrate here an integrated, straightforward and widely applicable approach to characterize cell type-specific transcriptional programs and regulatory mechanisms by generating two genome-wide data sets. We used deep sequencing of nuclear RNA (nucRNA-Seq) to comprehensively describe the nuclear transcriptome in ex vivo murine erythroid cells. In parallel, we generated a profile of active RNA polymerase II (RNAPII) binding by chromatin-immunoprecipitation (ChIP-Seq), allowing us to explore the relationship between RNAPII occupancy and transcriptional output in erythroid cells on a genome-wide scale. Comparative analysis of both data sets enables us to not only measure primary transcriptional output and identify genes associated with more efficient polymerase usage, but also to identify putative regulatory elements such as enhancers and novel non-coding transcripts. Application of this method to different cell types allows for the characterization of important aspects of gene regulation in a cell type-specific manner. Our findings demonstrate the complex ways in which RNAPII is associated with the genome and how this affects transcription of target genes, highlighting the importance of approaching transcriptome characterization from multiple angles.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 26 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
We hypothesize that germline variation influences susceptibility to aggressive prostate tumor
Publication Title
GNL3 and SKA3 are novel prostate cancer metastasis susceptibility genes.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
RRP1B is a breast cancer metastasis suppressor that interacts with various regulators of gene transcription
Publication Title
Metastasis-associated protein ribosomal RNA processing 1 homolog B (RRP1B) modulates metastasis through regulation of histone methylation.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Ndn is a candidate metastasis suppressor gene that has been reported to regulate transcription.
Publication Title
Necdin is a breast cancer metastasis suppressor that regulates the transcription of c-Myc.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Hypoxia-induced HIF1α targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
These datasets describe a melanocyte specific, HIF1A-Dependent / Hypoxia-Responsive gene expression signature defined by the regulation of genes critical to metabolism, chromatin and transcriptional regulation, vascularization and cellular invasivness. These genes provide lineage specific targets for refinement of diagnostic markers associated with primary melanoma tumor metastatic potential, and also provides novel molecular targets for therapeutic strategies targeting metastatic disease progression.
Publication Title
Hypoxia-induced HIF1α targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis.
Sample Metadata Fields
Specimen part, Cell line
View Samples- 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.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples