Filters
Technology
Platform
GSE30507
Populus trichocarpa
16 Downloadable Samples
Affymetrix Poplar Genome Array (poplar)
Description
Lignocellulosic feedstock (i.e., wood) is gaining popularity as a source of fermentable sugars for liquid fuel production. To improve the quantity and quality of woody biomass, the developing xylem (DX) cell-specific genetic modification is desired. Bioinformatic analyses followed by the validation of cell type-specific transcriptomes led to the identification of 37 transcripts specifically expressed in DX. After further confirmation of DX-specific expression, we selected four genes (DX5, DX8, DX11 and DX15) to demonstrate the feasibility of our strategy. The promoter regions of selected DX genes were isolated and produced stable transformants of poplar by using transcriptional promoter:-glucuronidase (GUS) fusion constructs. The GUS expression patterns of DX5 and ANAC073 (orthologous gene of Arabidopsis) revealed that these promoters were active in xylem cells in poplar at early seedling growth, and showed strongest expression in the developing xylem cells in the wood formation/development at later growth stages of poplar. DX specific and strong expression patterns of all the other DX promoters (DX8, DX11 and DX15) tested suggests that these promoters may be useful to control transgene expression in the DX cells of woody plants with the aim of the feedstock improvement.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 15 Downloadable Samples
- Illumina humanRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
No associated publication
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 9 Downloadable Samples
Illumina humanRef-8 v2.0 expression beadchip
Description
To investigate thapsigargin or tunicamycin-induced transcriptomes in SH-SY5Y cells
Publication Title
No associated publication
Sample Metadata Fields
Cell line, Treatment
View Samples- Arabidopsis thaliana
- 7 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
MYB46 functions as a transcriptional switch that turns on the genes necessary for secondary wall biosynthesis. Elucidating the transcriptional regulatory network immediately downstream of MYB46 is crucial to our understanding of the molecular and biochemical processes involved in the biosynthesis and deposition of secondary walls in plants. The transcription factors identified here may include direct activators of secondary wall biosynthesis genes. The current study discovered novel hierarchical relationships among the transcription factors involved in the transcriptional regulation of secondary wall biosynthesis and generated several testable hypotheses.
Publication Title
Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina humanRef-8 v2.0 expression beadchip
Description
To investigate atrazine induced transcriptomes in SH-SY5Y cells
Publication Title
No associated publication
Sample Metadata Fields
Cell line, Treatment
View Samples- Populus trichocarpa
- 4 Downloadable Samples
- Affymetrix Poplar Genome Array (poplar)
Description
Winter survival and maintenance strategy is crucial in temperate woody plants. Here, we demonstrate novel aspects of the transcriptional regulations adopted by perennial tree species in winter/dormancy, employing a biochemical and whole transcriptome analysis. As expected, genes related to cold hardiness and defense are over-represented. Interestingly, carbohydrate biosynthesis and transport-related genes were very actively expressed in winter/dormancy. Further biochemical analyses verified the dormancy/winter transcription phenotype. Furthermore, dormancy/winter preferential expression of genes involved in the cell wall biosynthesis/modification, circadian rhythm, the indirect transcriptional regulation (RNA metabolism), and chromatin modification/remodeling were identified. Taken together, regulation of gene expression in the winter survival and maintenance may include not only controlled by promoter binding transcription factors but may also be regulated at the post-transcriptional and chromatin levels.
Publication Title
Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of poplar.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Recently, AtC3H14, a CCCH-type zinc finger protein, was identified as one of the direct targets of MYB46, which is known as a master regulator of secondary wall biosynthesis. AtC3H14 and their homologs (i.e., AtC3H15 and PtrC3H14-1 from Arabidopsis and poplar, respectively) are predominantly expressed in the secondary wall forming tissues. Transgenic Arabidopsis plants overexpressing AtC3H14 (i.e., 35S::AtC3H14 plants) produced dwarfing phenotypes. 35S::AtC3H14 plants developed phloem fibers earlier than wild-type and this phenotype was more pronounced in the roots. Interestingly, ectopic secondary wall thickenings were found in both stems and roots. These phenotypic consequences are successively reproduced from the 35S::AtC3H15 and 35S::PtrC3H14-1 plants. Whole transcriptome GeneChip analysis identified that the cell wall and extracellular-related genes are extremely over-represented in the stem tissues of 35S::AtC3H14 plants. These results suggest that AtC3H14 may act as a negative regulator of cell elongation with modification of cell wall reassembly and be involved in the secondary wall formation in Arabidopsis.
Publication Title
AtC3H14, a plant-specific tandem CCCH zinc-finger protein, binds to its target mRNAs in a sequence-specific manner and affects cell elongation in Arabidopsis thaliana.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Neuroprotective changes of striatal degeneration-related gene expression by acupuncture in an MPTP mouse model of Parkinsonism: microarray analysis.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Acupuncture at acupoints GB34 and LR3 has been reported to inhibit nigrostriatal degeneration in parkinsonism models, yet the genes related to this preventive effect of acupuncture on the nigrostriatal dopaminergic system remain elusive.
Publication Title
Neuroprotective changes of striatal degeneration-related gene expression by acupuncture in an MPTP mouse model of Parkinsonism: microarray analysis.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
It has been shown that acupuncture at acupoints GB34 and LR3 inhibits the degeneration of nigrostriatal neurons in an 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of Parkinsons disease. This preventative effect of peripheral acupuncture stimulation is hypothesized to be transmitted through the spinal cord to the nigrostriatal neurons.
Publication Title
Changes of gene expression profiles in the cervical spinal cord by acupuncture in an MPTP-intoxicated mouse model: microarray analysis.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples