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accession-icon GSE12404
Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
  • organism-icon Arabidopsis thaliana
  • sample-icon 87 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE21684
Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis
  • organism-icon Arabidopsis thaliana
  • sample-icon 46 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5.

Publication Title

Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE44213
Transcriptional responses to water deficit and Xylella fastidiosa (Pierce's disease) in Vitis vinifera
  • organism-icon Vitis vinifera
  • sample-icon 45 Downloadable Samples
  • Technology Badge Icon Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)

Description

Pierces disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grapes. To test the long-standing hypothesis that Pierces disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a massive redirection of gene transcription involving 822 genes with a minimum 2-fold change (p<0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis related (PR) proteins, absisic acid (ABA)/jasmonic acid (JA)-responsive transcripts, and down-regulation of transcripts related to photosynthesis, growth and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis, and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlation of the classical concept of the disease triangle where environment impacts disease severity.

Publication Title

Water deficit modulates the response of Vitis vinifera to the Pierce's disease pathogen Xylella fastidiosa.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE50384
Comparison of transcriptomes in five varieties of citrus fruit
  • organism-icon Citrus reticulata, Citrus x paradisi, Citrus sinensis, Citrus limon
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Citrus Genome Array (citrus)

Description

To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon.

Publication Title

Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE21136
Genome response to tissue plasminogen activator in experimental ischemic stroke
  • organism-icon Rattus norvegicus
  • sample-icon 42 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE61766
Expression data from rhesus macaque blood CD8+ T cells
  • organism-icon Macaca mulatta
  • sample-icon 33 Downloadable Samples
  • Technology Badge Icon Affymetrix Rhesus Macaque Genome Array (rhesus)

Description

Immunization of macaques with simian immunodeficiency virus with deletions in nef (SIVnef) has been shown to elicit protective immunity to infection by pathogenic SIV, yet our understanding of the mechanisms that orchestrate protection and prevent pathogenesis remains limited. In the study, we utilize whole-genome transcriptional profiling to reveal molecular signatures of protective immunity in circulating CD8+ T cells of rhesus macaques vaccinated with SIVmac239nef and challenged with pathogenic SIVmac251.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE51615
Expression data from rhesus macaque colon, jejunum, and lung
  • organism-icon Macaca mulatta
  • sample-icon 32 Downloadable Samples
  • Technology Badge Icon Affymetrix Rhesus Macaque Genome Array (rhesus)

Description

The mucosa that lines the respiratory and gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the frontline of immune defense against HIV infection. Using the simian immunodeficiency virus (SIV) rhesus macaque model, we have performed a comparative analysis of host gene expression in the lung and GI mucosa in response to SIV infection and antiretroviral therapy.

Publication Title

Enhanced innate antiviral gene expression, IFN-α, and cytolytic responses are predictive of mucosal immune recovery during simian immunodeficiency virus infection.

Sample Metadata Fields

Specimen part

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accession-icon GSE46356
Expression data from mouse cecum
  • organism-icon Mus musculus
  • sample-icon 25 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

To adapt the lives of organisms to the day-night cycle, evolution has built a complex machinery, whose molecular components are able to anticipate and drive changes in organism behavior and metabolism. A mutual bidirectional interaction exists between circadian abnormalities and development of diseases.

Publication Title

Circadian clock regulates the host response to Salmonella.

Sample Metadata Fields

Age, Specimen part

View Samples
accession-icon GSE22824
Gene expression in retina and LGN of wild type and Chrnb2-/- mice
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Mice lacking the beta 2 subunit (Chrnb2) of the neuronal nicotinic acetylcholine receptor display altered retinal waves and disorganized projections of the retinal ganglion cells to the lateral geniculate nucleus (LGN). mRNA populations from retinas and LGN from Chrnb2-/-and wild type (C57BL/6J) mice were compared at 4 days postnatal, when RGC segregation to the LGN begins in WT mice. Retinal mRNAs were also compared at adulthood.

Publication Title

Mouse mutants for the nicotinic acetylcholine receptor ß2 subunit display changes in cell adhesion and neurodegeneration response genes.

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon GSE50040
Cross-talk between E. coli strains and a human colorectal adenocarcinoma-derived cell line
  • organism-icon Homo sapiens
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The deposit microarray data were generated in a study that comprehensively integrated gene expression profiles and metabolic responses of Caco-2 cells that incubated with either E. coli K-12 or O157:H7. The aim of this study is to examine the impact of colonic bacteria on the global gene expression regulation and metabolite levels of the host, and investigate the molecular mechanics of the E. coli/host interaction.

Publication Title

Cross-talk between E. coli strains and a human colorectal adenocarcinoma-derived cell line.

Sample Metadata Fields

Cell line, Treatment

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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