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refine.bio helps you build ready-to-use datasets with normalized transcriptome data from all of the world’s genetic databases.
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accession-icon SRP151693
SISE affect Rattus norvegicus renal Transcriptome
  • organism-icon Rattus norvegicus
  • sample-icon 29 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Sacha inchi (Plukenetia volubilis L.) extract change the gut microbiota and alleviate the development of hypertension in spontaneously hypertensive rats

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

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accession-icon SRP150561
RNA-seq of human gastric cancer cell line (AGS)
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

Transcriptomic sequencing of human gastric cancer cell line (AGS) upon citral treatment

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Disease, Cell line

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accession-icon SRP136224
zebrafish RNA-seq
  • organism-icon Danio rerio
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

To reveal the toxic mechanism of thifluzamide in zebrafish

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP115073
zebrafish Raw sequence reads
  • organism-icon Danio rerio
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIllumina HiSeq 2500

Description

The study was to unravel the complex toxic effects of chemical contaminants on the health of organisms as based on different levels of biological profling.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon SRP092151
RNAseq analysis of med18 and med20 roots infected with Fusarium oxysporum
  • organism-icon Arabidopsis thaliana
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The study aims to identify differences in gene expression in the root tissue of wild type Columbia-0 as well as Arabidopsis Mediator subunit mutants, med18 and med20 in response to the root pathogen Fusarium oxysporum. Roots were inoculated for 24 hours before harvesting for RNA isolation and paired end Illumina sequencing.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Disease, Disease stage, Treatment

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accession-icon GSE28895
Expression data from stomach of germ-free and gnotobiotic mice
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The aim of this study was to examine the role of indigenous lactobacilli in the physiological development of the stomach in mice using microarray analysis. In lactobacilli-associated gnotobiotic mice, an increased expression of the genes related to the muscle system development, such as nebulin and troponin, was observed. On the other hand, the expression of the gastrin gene dramatically decreased. A microarray analysis of the stomachs infected with H. pylori also showed both the up-regulation of muscle cell genes and the down-regulation of gastrin genes.

Publication Title

Role of indigenous lactobacilli in gastrin-mediated acid production in the mouse stomach.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP081188
Homo sapiens Transcriptome or Gene expression
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

human Transcriptomehuman Transcriptomehuman Transcriptomehuman Transcriptomehuman Transcriptome

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon SRP106521
Transcriptome Analysis of Male Drosophila melanogaster Exposed to Ethylparaben
  • organism-icon Drosophila melanogaster
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

This study revealed the EP impact on gene expression in fruit fly and provided new insight into the mechanisms of this response, which is helpful for understanding EP toxicity to humans.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE10091
Transcript-specific translational regulation in the unfolded protein response of Saccharomyces cerevisiae
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome S98 Array (ygs98)

Description

The accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER) causes stress and induces the unfolded protein response (UPR) which is characterised in part by the transcriptional induction of genes involved in assisting protein folding. Translational responses to ER stress have been less well described and here we report on a genome-wide analysis of translational regulation in the response to the ER stress-inducing agent dithiothreitol (DTT) in Saccharomyces cerevisiae. Although the observed polysome profiles were similar under control and ER stress conditions microarray analysis identified transcipt-specific translational regulation. Genes with functions in ribosomal biogenesis and assembly were translationally repressed under ER stress. In contrast mRNAs for known UPR genes, including the UPR transcription factor HAC1, the ER-oxidoreductase ERO1 and the ER-associated protein degradation (ERAD) gene DER1 were enriched in polysomal fractions under ER stress conditions. In addition, we show that splicing of HAC1 mRNA is required for efficient ribosomal loading and that Gcn2p is required for normal HAC1 splicing, so shedding light on the role of this protein kinase in the UPR pathway.

Publication Title

Transcript-specific translational regulation in the unfolded protein response of Saccharomyces cerevisiae.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP039377
The Transcriptomes of Natural Developmental Magnum in Chickens
  • organism-icon Gallus gallus
  • sample-icon 7 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The goal of this study is to obtain the transcriptomes of chicken magnum in different natural developmental stages. There are totally five stages researched in this study and they are named D1, D2, D3, D4 and L. D1 to D4 are the abbreviations of developmental stage 1 to developmental stage 4 and L means laying stage. D1 refers to the lag phase (about 7 weeks old) in which the magnum has very slight change; D2 refers to the early proliferation phase (about 13 weeks old); D3 refers to the late proliferation phase (about 16 weeks old); D4 refers to the early differentiation phase (about 17 weeks old).

Publication Title

No associated publication

Sample Metadata Fields

Age

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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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