We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells.
SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis.
No sample metadata fields
View SamplesDownsream of GRID2 in the mouse cerebellum.
Altered Actions of Memantine and NMDA-Induced Currents in a New Grid2-Deleted Mouse Line.
Sex, Age
View SamplesWe use gene expression data to provide a three-faceted analysis on the links between molecular subclasses of glioblastima, epithelial-to mesenchymal transition (EMT) and CD133 cell surface protein. The contribution of this paper is three-folded: First, we used a newly identified signature for epithelial-to-mesenchymal transition in human mammary epithelial cells, and demonstrated that genes in this signature have significant overlap with genes differentially expressed in all known GBM subtypes. However, the overlap between the genes up-regulated in the mesenchymal subtype of GBM and in the EMT signature was more significant than other GBM subtypes. Second, we provided evidence that there is a negative correlation between the genetic signature of EMT and that of CD133 cell surface protein, a putative marker for neural stem cells. Third, we studied the correlation between GBM molecular subtypes and the genetic signature of CD133 cell surface protein. We demonstrated that the mesenchymal and neural subtypes of GBM have the strongest correlations with the CD133 genetic signature. While the mesenchymal subtype of GBM demonstrates similarity with the signatures of both EMT and CD133, it also demonstrates some differences with each of these signatures that is partly due to the fact that the signatures of EMT and CD133 are inversely related to each other. Taken together this data sheds light on role of the mesenchymal transition and neural stem cells, and their mutual interaction, in molecular subtypes of glioblastoma multiforme.
Investigating the link between molecular subtypes of glioblastoma, epithelial-mesenchymal transition, and CD133 cell surface protein.
Specimen part
View SamplesSwiss-Webster B mouse postnatal day 4-5 primary cerebellar culture (pooled from litter mates) treated with sonic hedgehog (Shh), controls (veh), growth arrested (arrest), cycloheximide (cyc) for 1, 3 and 24 hours.
Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach.
Specimen part
View SamplesTraditional rice varieties found in India have many desirable characteristics. Amongst them, their differential responses to abiotic and biotic stresses are of great agricultural importance. Drought or osmotic stress is one of the major abiotic stresses afflicting crop plants in India. Indigenous varieties like Dagad deshi have been found to be drought resistant and, thereby, are being studied in great detail by plant breeders and biotechnologists alike. In this study, we have analyzed the transciptomes of two contrasting cultivars, i.e. Dagad deshi (tolerant) and IR20 (susceptible), under control and stress conditions to elucidate the differences in their responses to drought stress using Affymetrix microarray platform.
Reference genes for accurate gene expression analyses across different tissues, developmental stages and genotypes in rice for drought tolerance.
Specimen part, Time
View SamplesAldosterone is known to have a number of direct adverse effects on the heart, including fibrosis and myocardial inflammation. However, genetic mechanisms of aldosterone action on the heart remain unclear.
Effect of acute aldosterone administration on gene expression profile in the heart.
No sample metadata fields
View SamplesOne third to one half of all infants born before the 28th wek of gestation develop BPD bronchopulmonary dysplasia. Our objective is to evaluate the feasibility of using expression profiling in umbilical cord tissue to discover molecular signatures for developmental staging and for risk of BPD.
Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia.
No sample metadata fields
View SamplesTranscriptome profile of highly purified multipotential (P), erythroid (E), and myeloid (M) bone marrow progenitors from three RPS19 mutated Diamond-Blackfan anemia and six control human subjects.
Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemia.
Sex, Age, Specimen part, Disease, Subject
View Sampleswe performed RNA sequencing analysis using 10 tissue samples from human prostate and evaluated efficiency and accuracy of eRNA on mRNA-seq data analysis. Overall design: We sequenced mRNAs from the 10 human tissue samples. After that, we identified mRNAs in these samples against known human genes.
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.
No sample metadata fields
View SamplesAffymetrix MG430 2.0 expression levels of wild-type (STHdhQ7/Q7), 3NP-treated wild-type (STHdhQ7/Q7+3-NP), and mutant (STHdhQ111/Q111) striatal cells
Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism.
No sample metadata fields
View Samples