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accession-icon GSE4289
Host transcriptome changes associated with episome loss and selection of keratinocytes containing integrated HPV16
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Integration of high-risk human papillomavirus (HRHPV) into the host genome is a key event in cervical neoplastic progression. Integration is associated with deregulated expression of the viral oncogenes E6 and E7 and acquisition of a selective growth advantage for cells containing integrants. Overexpression of the viral transcriptional regulator E2 from heterologous promoters has an inhibitory effect on transcription from integrated HRHPV. We therefore hypothesised that loss of E2-expressing episomes from cells in which integration had previously occurred would be required for such cells to gain a growth advantage. Using the unique W12 model of cervical squamous carcinogenesis, we show that cells containing integrated HPV16 reproducibly emerged during long-term culture when there had been a rapid fall in episome numbers. During the period of emergence it is possible to isolate single-cell clones containing an intracellular mixture of the integrant being selected and episomes at reduced load. Microarray analysis showed that episome loss was closely associated with endogenous activation of antiviral response genes that are also inducible by the type I interferon (IFN) pathway. Taken together, our results indicate that episome loss, associated with induction of antiviral response genes, is a key event in the spontaneous selection of cervical keratinocytes containing integrated HPV16. We conclude that cervical carcinogenesis requires not only HRHPV integration, but also loss of inhibitory episomes.

Publication Title

Selection of cervical keratinocytes containing integrated HPV16 associates with episome loss and an endogenous antiviral response.

Sample Metadata Fields

No sample metadata fields

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accession-icon E-MEXP-3267
Ruberti A.thaliana Shade Avoidance Response wt and phyA
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Aim of the experiment is the identification of genes differentially regulated in phyA seedlings relative to wild type after prolonged exposure to low R/FR. To this end, gene expression changes were analysed in Arabidopsis wild-type and phyA knock-out mutant seedlings exposed to low R/FR light. The experiment was designed to enable comparison between the different genotypes exposed or not exposed to low R/FR light.

Publication Title

No associated publication

Sample Metadata Fields

Age, Disease, Disease stage, Cell line, Time

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accession-icon E-MEXP-3266
Ruberti A. thaliana Intermediate molecular events in plant responses to canopy shade
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Aim of the experiment is the analysis of early and late molecular events in plant response to canopy shade. To this end, gene expression changes were analysed in Arabidopsis seedlings after exposure to low R/FR light for 4 hours and 1 day. The experiment was designed to enable comparison between treated and untreated Arabidopsis seedlings.

Publication Title

No associated publication

Sample Metadata Fields

Age, Time

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accession-icon GSE22207
Identification of promoter sequence elements involved in specific recognition by the S subunit of bacterial RNA polymerase.
  • organism-icon Escherichia coli str. k-12 substr. mg1655
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix E. coli Genome 2.0 Array (ecoli2)

Description

Promoter recognition by bacterial RNA polymerase is mediated by subunits, which assemble transiently to RNA polymerase core enzyme (E) during transcription initiation. subunits drive transcription of specific sets of genes by allowing RNA polymerase to interact with different promoter sequences. However, 70, the housekeeping subunit, and S, an alternative subunit mainly active during slow growth and in response to cellular stresses, appear to recognize almost identical promoter sequences, raising the question of how promoter selectivity is achieved in the bacterial cell. To identify sequence determinants for selective promoter recognition, we performed a run-off/microarray experiment (ROMA): in vitro transcription experiments were carried out with RNA polymerase saturated either with 70 (E70) or with S (ES) using the whole Escherichia coli genome as DNA template, and transcript levels were determined by microarray analysis. We found that several genes associated with bacterial growth (e.g., ribosomal operons) were transcribed more efficiently by E70. In contrast, ES transcribed preferentially genes involved in stress responses, secondary metabolism, as well as regulatory RNAs and intergenic regions with yet unknown function. Genes preferentially recognized in vitro by ES showed reduced expression in ES -deficient mutant strain of E. coli. Sequence comparison of E70- versus ES dependent promoters confirms that the presence of a -35 sequence and the relative location of UP elements affect promoter interaction with either form of RNA polymerase, and suggests that a G/C bias in the -2/+1 nucleotides would favour efficient promoter recognition by E70.

Publication Title

In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements.

Sample Metadata Fields

Disease

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accession-icon GSE14204
25-hydroxycholesterol effects on human hepatocyte metabolism and the antiviral state it conveys against the HCV
  • organism-icon Homo sapiens
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Hepatitis C virus (HCV) infection is a global health problem. A number of studies have implicated a direct role of cellular lipid metabolism in the HCV life cycle and inhibitors of the mevalonate pathway have been demonstrated to result in an antiviral state within the host cell. Transcriptome profiling was also conducted on Huh-7 human hepatoma cells bearing subgenomic HCV replicons with and without treatment with 25-hydroxycholesterol (25-HC), an inhibitor of the mevalonate pathway that alters lipid metabolism, to assess metabolic determinants of pro- and antiviral states within the host cell.

Publication Title

Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE106931
Expression data from cerebral CD163+ perivascular and meningeal macrophages (PV) obtained from controls (C) and ischemic (I) rats
  • organism-icon Rattus norvegicus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

We used adult male Sprague-Dawley rats (280-329 g body weight). Controls were nave rats. Ischemic rats were subjected to 1-hour occlusion of the right middle cerebral artery and 16h reperfusion.

Publication Title

CNS-border associated macrophages respond to acute ischemic stroke attracting granulocytes and promoting vascular leakage.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE108268
Expression data from Huh7.5 hepatoma cells transfected with 100 nM miR-7 mimic
  • organism-icon Homo sapiens
  • sample-icon 1 Downloadable Sample
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

Our work demonstrated that PPAR- regulates miR-7, a microRNA which regulates SREBP1 signaling.

Publication Title

No associated publication

Sample Metadata Fields

Cell line

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accession-icon GSE5131
Adjudin-induced germ cell loss from adult rat testes
  • organism-icon Rattus norvegicus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

This is a study to explore the transcriptional changes after Adjudin treatment in adult rat testes at three time points (control, 8 hour and 4 day). Adjudin, [1-(2,4-dichlorobenzyl)-1H-indazole-3-carbohydrazide], is a potential male contraceptive that targets the Sertoli-germ cell interface and causes germ cell depletion from the seminiferous epithelium. Adjudin has been proved to be a useful model to study the mechanisms that regulate junction restructuring in the testis.

Publication Title

Unraveling the molecular targets pertinent to junction restructuring events during spermatogenesis using the Adjudin-induced germ cell depletion model.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE9480
Expression data from adult rat testes treated with 3 mg/kg b.w. cadmium chloride via i.p.
  • organism-icon Rattus norvegicus
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

This is a study to explore the transcriptional changes after cadmium treatment in adult rat testes at three time points (control--0 hour, 8 hour and 4 day). Cadmium is an environmental toxicant that is known to affect the male reproductive system. It disrupts the blood-testis barrier irreversibly, and affects the Sertoli-germ cells adhesion, causing germ cell depletion from the seminiferous epithelium.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE8925
Global expression profiling to study the effect of imidazolinone herbicide treatment on Arabidopsis thaliana
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Using whole genome microarray (Affymetrix ATH1) we studied the transcriptional response of Arabidopsis thaliana to imidazolinone (Arsenal) herbicde that inhibits acetolactate synthase (ALS) enzyme and thus disrupts branched chain amino acid biosynthesis. A number of genes related to amino acid, protein metabolism, growth, regulatory networks, respiratory pathways, stress, defense and secondary metabolism were altered.

Publication Title

A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus.

Sample Metadata Fields

No sample metadata fields

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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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