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accession-icon GSE64755
Global transcriptome analysis identifies shade avoidance-related genes regulated by BBX24 in Arabidopsis thaliana
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

In seedlings, the induction of shade avoidance syndrome (SAS) involves a rapid up-regulation for known shade marker genes and subsequently activates an interacting network of various hormones that will eventually lead to cell elongation. We found that the B-box protein AtBBX24 have positive effects on the SAS (positive regulators). Global expression analysis of col and bbx24 seedlings reveals that a large number of genes involved in hormonal signaling pathways are positively regulated by BBX24 in response to simulated shade.

Publication Title

The transcriptional regulator BBX24 impairs DELLA activity to promote shade avoidance in Arabidopsis thaliana.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE6509
Gene Profile of RU486 effect on LPS induced gene expression in CNS.
  • organism-icon Mus musculus
  • sample-icon 37 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

The study was designed in order to identify genes differentially expressed when glucocorticoid signaling is blocked by a glucocorticoid-receptor antagonist (RU486 mifepristone) in the context of brain inflammation induced by bacterial lipopolysaccharide (LPS). LPS is only able to cause murine brain damage in our experimental conditions upon RU486 pre-treatment. Hence, the study may reveal potential candidate genes to mediate neuroprotection or neurotoxicity. Due to the factorial design of the experiment, RU486 main-effect could be dissociated from the effects resultant of RU486/inflammation interaction. In addition, brain dissection was conducted to verify the effects in the brain side ipsilateral or contralateral to the site of intracerebral LPS infusion.

Publication Title

Genes involved in the balance between neuronal survival and death during inflammation.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE39819
Transcriptional response of bovine macrophages after infection with two Argentinean Mycobacterium bovis isolates
  • organism-icon Bos taurus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Bovine Genome Array (bovine)

Description

Infection of cattle with Mycobacterium bovis causes severe financial hardship in many countries, in addition to presenting a health risk for humans. As an intracellular pathogen, M. bovis, adapted to survive and thrive within the intramacrophage environment. However, little is known about expression patterns in the macrophage, particularly in the bovine host.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE18808
A methyl transferase links the circadian clock to the regulation of alternative splicing
  • organism-icon Drosophila melanogaster, Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Study on differential gene expression and splicing between wildtype and clock mutants. This study is part of a comparative analysis of the role of Protein Methyltransferase 5 in the regulation of transcriptional and post-transcriptional processes simultaneously in Arabidopsis and Drosophila.

Publication Title

A methyl transferase links the circadian clock to the regulation of alternative splicing.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE75744
Effect of Cathepsin L exposure on endothelial cell transcriptomics
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Cathepsin L is a lysosomal protease that is secreted by several cancer cells. Cathepsin L upregulation has been widely associated with poor clinical outcome and increased metastatic incidence. However, whether Cathepsin L participates in tumor angiogenesis remains less studied. Our study showed a significant activation of angiogenic capacity of endothelial cells in presence of purified or tumor derived Cathepsin L. In addition, Cathepsin L exposure led to a significant increase in the proliferative capacity of endothelial cells. While the ability of Cathepsin L to promote endothelial cell sprouting, migration, invasion and tube formation can be attributed to its proteolytic effects on extracellular matrix, how it promotes endothelial cell proliferation remains obscure. The objective of this study was to test if Cathepsin L exposure can activate signaling cascades and gene expression leading to proliferation of endothelial cells.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Cell line, Treatment

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accession-icon GSE21601
Expression data from Arabidopsis thaliana
  • organism-icon Arabidopsis thaliana
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Nitrogen and light are two major regulators of plant metabolism and development. While genes involved in the control of each of these signals have begun to be identified, regulators that integrate gene responses to nitrogen and light signals have yet to be determined.

Publication Title

Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE38102
Expression data from Oryza sativa and Arabidopsis thaliana
  • organism-icon Oryza sativa, Arabidopsis thaliana
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana, ecotype Columbia-0) to a crop, rice (Oryza sativa spp. japonica (Nipponbare)), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants.

Publication Title

Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE46741
Arabidopsis circadian regulatory networks
  • organism-icon Arabidopsis thaliana
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator.

Sample Metadata Fields

Specimen part, Treatment, Time

View Samples
accession-icon GSE46621
Expression data from Arabidopsis thaliana seedlings
  • organism-icon Arabidopsis thaliana
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Light pulses at the end of the day or night be able to control the phase of the circadian clock. Pulses in the middle of the night has not effect on the circadian oscilations.

Publication Title

LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator.

Sample Metadata Fields

Specimen part, Treatment, Time

View Samples
accession-icon GSE73072
Host gene expression signatures of H1N1, H3N2, HRV, RSV virus infection in adults
  • organism-icon Homo sapiens
  • sample-icon 2886 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

Consider the problem of designing a panel of complex biomarkers to predict a patient's health or disease state when one can pair his or her current test sample, called a target sample, with the patient's previously acquired healthy sample, called a reference sample. As contrasted to a population averaged reference, this reference sample is individualized. Automated predictor algorithms that compare and contrast the paired samples to each other could result in a new generation of test panels that compare to a person's healthy reference to enhance predictive accuracy. This study develops such an individualized predictor and illustrates the added value of including the healthy reference for design of predictive gene expression panels. The objective is to predict each subject's state of infection, e.g., neither exposed nor infected, exposed but not infected, pre-acute phase of infection, acute phase of infection, post-acute phase of infection. Using gene microarray data collected in a large-scale serially sampled respiratory virus challenge study, we quantify the diagnostic advantage of pairing a person's baseline reference with his or her target sample.

Publication Title

An individualized predictor of health and disease using paired reference and target samples.

Sample Metadata Fields

Specimen part, Subject, Time

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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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Developed by the Childhood Cancer Data Lab

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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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