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GSE30941
Oryza sativa
15 Downloadable Samples
Affymetrix Rice Genome Array (rice)
Description
Magnaporthe oryzae is the causative agent of the rice blast, the most relevant rice disease worldwide. To date expression analysis on rice infected with Magnaporthe oryzae have been carried out only with the strains FR13 (leaf) and Guy 11 (root). However different strains of Magnaporthe are present in the environment leading to different rice responses at molecular level. To gain more insight on the unknown molecular mechanisms activated by different Magnaporthe strains during rice defense, a global expression analysis was performed by using the GeneChip Rice Genome Array.
Publication Title
OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 6 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Powdery mildew is a very common plant disease and only few plants are immune. Host interactions have been identified and characterized for the pathosystems barley-B. graminis f. sp. tritici (Bgt) and wheat-B. graminis f. sp. hordei (Bgh), whereas no data are reported about powdery mildew and nonhost plants, such as rice. On the other hand rice nonhost resistance is widely unexploited and only few expression data are available. To characterize rice response during nonhost interaction with Bgh, a global expression analysis was performed by using the GeneChip Rice Genome Array.
Publication Title
OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 16 Downloadable Samples
IlluminaHiSeq2500
Description
Myelin-reactive T cells have been identified in patients with multiple sclerosis (MS) and healthy subjects with comparable frequencies, but the contribution of these autoreactive T cells to disease pathology remains unknown. A total of 13,324 T cell libraries generated from blood of 23 patients and 22 healthy controls were interrogated for reactivity to myelin antigens. Libraries derived from CCR6+ myelin-reactive T cells from patients with MS exhibited significantly enhanced production of IFN-?, IL-17, and GM-CSF compared to healthy controls. Single-cell clones isolated by MHC/peptide tetramers from CCR6+ T cell libraries also secreted more pro-inflammatory cytokines while clones isolated from controls secreted more IL-10. The transcriptomes of myelin-specific CCR6+ T cells from patients with MS were distinct from those derived from healthy controls, and of note, were enriched in Th17-induced experimental autoimmune encephalitis (EAE) gene signatures and gene signatures derived from Th17 cells isolated other human autoimmune diseases. These data, although not casual, imply that functional differences between antigen specific T cells from MS and healthy controls is fundamental to disease development and support the notion that IL-10 production from myelin-reactive T cells may act to limit disease progression, or even pathogenesis. Overall design: Four conditions of purified T cells with between 3 and 5 replicates per condition
Publication Title
Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Deregulation of the transforming growth factor- (TGF) signaling pathway in epithelial ovarian cancer has been reported, but the precise mechanism underlying disrupted TGF signaling in the disease remains unclear. We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate genome-wide screening of TGF-induced SMAD4 binding in epithelial ovarian cancer. Following TGF stimulation of the A2780 epithelial ovarian cancer cell line, we identified 2,362 SMAD4 binding loci and 318 differentially expressed SMAD4 target genes. Comprehensive examination of SMAD4-bound loci, revealed four distinct binding patterns: 1) Basal; 2) Shift; 3) Stimulated Only; 4) Unstimulated Only. SMAD4-bound loci were primarily classified as either Stimulated only (74%) or Shift (25%), indicating that TGF-stimulation alters SMAD4 binding patterns in epithelial ovarian cancer cells compared to normal epithelial cells. Furthermore, based on gene regulatory network analysis, we determined that the TGF-induced SMAD4-dependent regulatory network was strikingly different in ovarian cancer compared to normal cells. Importantly, the TGF/SMAD4 target genes identified in the A2780 epithelial ovarian cancer cell line were predictive of patient survival, based on in silico mining of publically available patient data bases. In conclusion, our data highlight the utility of next generation sequencing technology to identify genome-wide SMAD4 target genes in epithelial ovarian cancer. The results link aberrant TGF/SMAD signaling to ovarian tumorigenesis. Furthermore, the identified SMAD4 binding loci, combined with gene expression profiling and in silico data mining of patient cohorts, may provide a powerful approach to determine potential gene signatures with biological and future translational research in ovarian and other cancers.
Publication Title
ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer.
Sample Metadata Fields
Cell line, Treatment
View Samples- Glycine max
- 35 Downloadable Samples
- Illumina HiSeq 2000
Description
By sequencing 36 cDNA libraries with Illumina technology, we identified genes differentially expressed in soybean plants in response to water deficit and genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes (Glyma v1.1), 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants. Overall design: Gene expression analysis of soybean leaves under water deficit in 6 periods of day by sequencing 36 libraries, in triplicate, in Illumina platform.
Publication Title
Daytime soybean transcriptome fluctuations during water deficit stress.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 26 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Gene expression (by Affymetrix GeneChip Human 1.0ST) profiling of biopsy samples from recurrent, platinum resistant epithelial ovarian cancer patients before and after treatment of decitabine in combination with carboplatin. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in PBMC (14 paired samples), tumor (8 paired samples) and ascites (6 paired samples) (GSE31826).
Publication Title
Decitabine reactivated pathways in platinum resistant ovarian cancer.
Sample Metadata Fields
Age
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Mouse model for Fetal Alcohol Syndrome. Embryos exposed to alcohol in controlled environment to assess teratogenic effects.
Publication Title
Identification of transcription factor and microRNA binding sites in responsible to fetal alcohol syndrome.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We hypothesize that gene expression in the cigarette smoke (CS) exposed neonatal lung and age-matched controls will be divergent. CS exposed lung will have divergence of immune response genes and structural genes. The lungs of (6) 2 week old neonatal mice exposed to 2 weeks of CS were compared to the lung of (4) 2 week old age-matched control mice. We utilized microarray analysis to examine transcriptional differences between smoke exposed neonatal lung and age-matched controls.
Publication Title
Impaired lung homeostasis in neonatal mice exposed to cigarette smoke.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Cisplatin and carboplatin are the primary first-line therapies for the treatment of ovarian cancer. However, resistance to these platinum-based drugs occurs in the large majority of initially responsive tumors, subsequently resulting in a poor long-term prognosis. To model the onset of drug resistance, we measured gene expression alterations associated with cisplatin resistance.
Publication Title
Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer.
Sample Metadata Fields
Cell line
View Samples