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GSE31456
Mus musculus
20 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Transcriptional programming of cell identity promises to open up new frontiers in regenerative medicine by enabling the efficient production of clinically relevant cell types. We examine if such cellular programming is accomplished by transcription factors that each have an independent and additive effect on cellular identity, or if programming factors synergize to produce an effect that is not independently obtainable. The combinations of Ngn2-Isl1-Lhx3 and Ngn2-Isl1-Phox2a transcription factors program embryonic stem cells to express a spinal or cranial motor neuron identity respectively. The two alternate expression programs are determined by recruitment of Isl1/Lhx3 and Isl1/Phox2a pairs to distinct genomic locations characterized by two alternative dimeric homeobox motifs. These results suggest that the function of programming modules relies on synergistic interactions among transcription factors and thus cannot be extrapolated from the study of individual transcription factors in a different cellular context.
Publication Title
Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity.
Sample Metadata Fields
Cell line, Treatment
View Samples- Oryza sativa
- 11 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Salt Stress response of salt-tolerant genotype FL478 compared to IR29
Publication Title
Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress.
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare
- 24 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Salt Stress response of salt-tolerant genotype Golden Promise compared to Maythorpe
Publication Title
Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise.
Sample Metadata Fields
No sample metadata fields
View Samples- Hordeum vulgare
- 21 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Detection of single feature polymorphisms comparing five barley genotypes. Gene expression under unstressed and drought stressed conditions.
Publication Title
Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Gene expression was measured from the dentate gyrus and entorhinal cortex harvested from human postmortem samples.
Publication Title
Molecular mechanism for age-related memory loss: the histone-binding protein RbAp48.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Oryza sativa indica group
- 23 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Analysis of root gene expression of salt-tolerant genotypes FL478, Pokkali and IR63731, and salt-sensitive genotype IR29 under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in indica rice.
Publication Title
Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Study of the gene expression of T24 bladder cancer cells in response to hypericin-mediated photodynamic therapy in the absence or presence of the p38 MAPK inhibitor PD169316
Publication Title
Molecular effectors and modulators of hypericin-mediated cell death in bladder cancer cells.
Sample Metadata Fields
Specimen part, Cell line, Compound
View Samples- Oryza sativa, Zea mays, Hordeum vulgare, Sorghum bicolor, Triticum aestivum, Avena sativa
- 8 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
This study was conducted to evaluate the efficiency of cross-species detection in Barley1 GeneChip array. We hybridized cRNA derived from first leaves of barley green seedlings (as a control), as well as the same stage of seedling leaf from representative genotypes of wheat, oat, rice, maize, and sorghum. Ten to twenty seedlings for each species were harvested and pooled for RNA preparation, labeling, and hybridization. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB1 at PLEXdb.]
Publication Title
A new resource for cereal genomics: 22K barley GeneChip comes of age.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Alternative mRNA splicing is the main reason vast mammalian proteomic complexity can be achieved with a limited number of genes. Splicing is physically and functionally coupled to transcription and the rate of transcript elongation has a profound effect on splicing. As the nascent pre-mRNA emerges from transcribing RNA polymerase II (RNAPII), it is assembled into a messenger ribonucleoprotein (mRNP) particle that represents its functional form, and the composition of which determines the fate of the mature transcript4. However, factors that connect the transcribing polymerase with the mRNP particle and help integrate transcript elongation with mRNA splicing remain obscure. Here, we characterized the interactome of chromatin-associated mRNP particles and thereby identified Deleted in Breast Cancer 1 (DBC1) and a protein we named ZIRD. These proteins are subunits of a novel protein complex, named DBIRD, which binds directly to RNAPII. DBIRD regulates alternative splicing of a large set of exons embedded in A/T-rich DNA, and is present at the affected exons. RNAi-mediated DBIRD depletion results in region-specific decreases in transcript elongation, particularly across areas encompassing affected exons. These data indicate that DBIRD complex acts at the interface between mRNP particles and RNAPII, integrating transcript elongation with regulation of alternative splicing.
Publication Title
DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation.
Sample Metadata Fields
Cell line
View Samples- Hordeum vulgare
- 32 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip.
Publication Title
Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools.
Sample Metadata Fields
No sample metadata fields
View Samples