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accession-icon GSE6737
Over-expression of a Type-A Response Regulator Alters Rice Morphology and Cytokinin Metabolism
  • organism-icon Oryza sativa
  • sample-icon 27 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE6719
Cytokinin responsive genes in rice
  • organism-icon Oryza sativa
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Cytokinins (CKs) are a class of plant hormones that regulate many aspects of growth and development, including cell division, apical dominance, leaf senescence, nutrient signaling, and shoot differentiation. In the past decade, substantial progress has been made in understanding CK biosynthesis, metabolism and signal transduction. Much of this knowledge is based on research in Arabidopsis, a dicotyledonous model plant. Although cytokinin plays an important role for growth and development in the Gramineae, our knowledge of cytokinin responsive genes in monocotyledonous species is very limited compared to Arabidopsis. The search for genes whose expression is modified by CK has yielded a number of valuable tools that have been used to understand CK signaling and the complex developmental processes under control of this hormone. We tried to identify rice genes regulated by CK using an Affymetrix rice genome array.

Publication Title

Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE6720
Gene expression in OsRR6-overexpression line
  • organism-icon Oryza sativa
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Cytokinins (CKs) are a class of plant hormones that regulate many aspects of growth and development, including cell division, apical dominance, leaf senescence, nutrient signaling, and shoot differentiation. In the past decade, substantial progress has been made in understanding CK biosynthesis, metabolism and signal transduction. Much of this knowledge is based on research in Arabidopsis, a dicotyledonous model plant. The current model of the CK signaling pathway is a multi-step His-Asp phosphorelay system. Some of the cytokinin-inducible response regulators are thought to act as negative regulators of CK signaling. We tried to identify rice genes regulated by CK-inducible response regulator using an Affymetrix rice genome array and transgenic rice that over-express OsRR6.

Publication Title

Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE37056
Expression data from fosb gene modified mouse
  • organism-icon Mus musculus
  • sample-icon 28 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

To examine fosB regulation of neurogenesis, depression and epilepsy, we compared the gene expression profiles of wild type, fosBd/d and fosB-null mice by microarray analysis.

Publication Title

fosB-null mice display impaired adult hippocampal neurogenesis and spontaneous epilepsy with depressive behavior.

Sample Metadata Fields

Sex, Age, Specimen part, Treatment

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accession-icon GSE15046
Transcriptome analysis of gibberellin-signaling mutants in rice [Oryza sativa]
  • organism-icon Oryza sativa
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Gibberellins control a wide range of aspects of plant growth and development. Although a series of mutant of the signaling pathway has been identified, the global regulatory network underlying gibberellin signal transduction has not been revealed. To address this issue, we performed microarray analysis with rice gibberellin signaling mutants, gid1, gid2, slr, and the parental cultivar Taichung 65.

Publication Title

Highly sensitive and high-throughput analysis of plant hormones using MS-probe modification and liquid chromatography-tandem mass spectrometry: an application for hormone profiling in Oryza sativa.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE60933
Ileal gene expression in Duoxa-/- mice and cohoused littermate controls
  • organism-icon Mus musculus
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Dual oxidases play a role in innate host defense at barrier epithelia. We examined the effect of loss of dual oxidase function (duoxa-/-) on gene expression in the mouse terminal ileum at homeostasis. To control for cage/litter effects, duoxa-/- were cohoused with wild type littermate controls.

Publication Title

Increased Expression of DUOX2 Is an Epithelial Response to Mucosal Dysbiosis Required for Immune Homeostasis in Mouse Intestine.

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon GSE89440
Interferon stimulation creates chromatin marks to establish transcriptional memory
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Interferon stimulation creates chromatin marks and establishes transcriptional memory.

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE73882
Functional characterization of inflammatory bowel disease-associated gut dysbiosis in gnotobiotic mice
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.1 ST Array (mogene21st)

Description

Gut dysbiosis is closely involved in the pathogenesis of inflammatory bowel disease (IBD). However, it remains unclear whether IBD-associated gut dysbiosis plays a primary role in disease manifestation or is merely secondary to intestinal inflammation. Here, we established a humanized gnotobiotic (hGB) mouse system to assess the functional role of gut dysbiosis associated with two types of IBD - Crohn's disease (CD) and ulcerative colitis (UC).

Publication Title

Functional Characterization of Inflammatory Bowel Disease-Associated Gut Dysbiosis in Gnotobiotic Mice.

Sample Metadata Fields

Specimen part

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accession-icon GSE79067
To determine transcriptome of gnotobiotic mice fed fiber-rich and fiber-free diets
  • organism-icon Mus musculus
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.1 ST Array (mogene21st)

Description

Despite accepted health benefits of dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and alters disease risk. Using a gnotobiotic model, in which mice were colonized with a synthetic human gut microbiota, we elucidated the functional interactions between dietary fiber, the gut microbiota and the colonic mucus barrier, which serves as a primary defence against pathogens. We show that during chronic or intermittent dietary fiber deficiency, the gut microbiota resorts to host-secreted mucus glycoproteins as a nutrient source, leading to erosion of the colonic mucus barrier. Dietary fiber deprivation promoted greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium, but only in the presence of a fiber-deprived microbiota that is pushed to degrade the mucus layer. Our work reveals intricate pathways linking diet, gut microbiome and intestinal barrier dysfunction, which could be exploited to improve health using dietary therapeutics.

Publication Title

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE52430
Gene expression profiles of lymphoma cells in homozygous Tet2 gene trap mice and CD4+ control cells.
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

TET2 is an enzyme for converting methylcytosine (mC) to hydorxymethylcytosine (hmC) and its mutations have been frequently found in myeloid malignancies and T-cell lymphoma in humans. We analyzed Tet2 gene trap mice and found that homozygous mice developed T-cell lymphoma with follicular helper T-cell-like features.

Publication Title

Reduced TET2 function leads to T-cell lymphoma with follicular helper T-cell-like features in mice.

Sample Metadata Fields

Specimen part

View Samples
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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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