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accession-icon SRP007813
Glycine max Transcriptome or Gene expression
  • organism-icon Glycine max
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

Background: Plants, involved in highly complex and well-coordinated system, have evolved a considerable degree of developmental plasticity, thus minimize the damages caused by stresses. MicroRNAs (miRNAs) have recently emerged as key regulators in gene regulation, developmental processes and stress tolerance in plants. Results: In this study, systematic discovery of soybean miRNAs associated with stress response (mock, drought, salinity and alkalinity) has been identified and analyzed in combination with deep sequencing technology and in-depth bioinformatics analysis. We found that a total of 133 conserved miRNAs corresponding to 95 miRNA families have expressed in soybean under four diverse treatments. In addition, 71, 50 and 45 miRNAs are either uniquely or differently expressed under drought, salinity and alkalinity respectively, suggesting that many miRNAs are inducible and are differentially expressed in response to certain stress. Conclusion: Our study has important implications for further identification of gene regulation under abiotic stresses and also significantly contributes a complete profile of miRNAs in Glycine max.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE43576
Expression data from Human primary colon cancer cells
  • organism-icon Homo sapiens
  • sample-icon 3 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Transcriptional profiling of Human primary colon cancer cells under spheroid culture. Goal was to determine the effects of spheroid culture on global primary colon cancer cells gene expression.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-43576

Sample Metadata Fields

Specimen part

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accession-icon GSE95506
Expression data from human myocardial cells, AC16
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

This study aimed to provide new compelling clues in the PM2.5-induced toxicity and mechanism which order the meaningful bioinformatics evidences for further study on human cardiovascular system.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-95506

Sample Metadata Fields

Specimen part, Cell line, Treatment

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accession-icon GSE90896
Expression data of LncRNA from the rat knee articular cartilage at different developmental stages
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

We performed microarray analysis to compare the gene expression profile of sunitinib-treated primary xenograft tumors (sensitive or resistant status) with that of vehicle-treated.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-90896

Sample Metadata Fields

Specimen part

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accession-icon SRP163233
Transcriptome profile in bursa of Fabricius reveals potential mode for stress-influenced immune function in chickens
  • organism-icon Gallus gallus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

The molecular mechanisms underlying stress-influenced immune function are not clear. Chicken stress models can be established effectively by feeding chickens corticosterone hormone. The bursa of Fabricius is a unique central immune organ of birds. RNA sequencing (RNA-Seq) technology was used to investigate differences in the expression profiles of immune-related genes and associated pathways in the bursa of Fabricius to clarify molecular mechanisms. The aim of this study was to broaden the understanding of the stress-influenced immune function in chickens.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE62399
Genome-wide expression profiling after Allyl Alcohol treatment in Saccharomyces cerevisiae
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

Allyl alcohol is a highly toxic industrial chemical used as a synthetic substrate, and as an herbicide in agriculture. It is evident that Allyl alcohol is metabolized by alcohol dehydrogenases (ADH) to the highly toxic Acrolein. Acrolein is a simple unsaturated aldehyde, ubiquitous environmental pollutant, endogenous metabolite and major constituent of cigarette smoke. Acrolein is highly electrophilic in nature and has strong reactivity towards nucleophiles present in cell such as amino acids, proteins and DNA.

Publication Title

Molecular cytotoxicity mechanisms of allyl alcohol (acrolein) in budding yeast.

Alternate Accession IDs

E-GEOD-62399

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE62400
Genome-wide expression profiling after Valproic acid treatment in Saccharomyces cerevisiae
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

Valproic acid (VA) is a small-chain branched fatty acid, widely used as anticonvulsant, and mood stabilizer to treat psychiatric illness. Valproic acid is also known to inhibit the histone deacetylases (HDACs), which makes it as a potent antitumor agent in alone or in combination with other cytotoxic drugs. Beside its conventional activities, valproic acid reported to have much broader, complicated effects and affect many complex physiological processes. However the molecular mechanisms of valproic acid are unclear.

Publication Title

Combined Transcriptomics and Chemical-Genetics Reveal Molecular Mode of Action of Valproic acid, an Anticancer Molecule using Budding Yeast Model.

Alternate Accession IDs

E-GEOD-62400

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE76985
Genome-wide monitoring of gene expression in Saccharomyces cerevisiae upon KP1019 treatment
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

KP1019 (trans-[tetrachlorobis(1H-indazole) ruthenate(III)]) is a ruthenium complex that exhibited anti-cancer activity in several in vitro and in vivo studies. KP1019 was even efficient against cancer cells that were resistant to other chemotherapeutic agents and thus emerged as a promising anti-cancer drug without dose-limiting cytotoxicity. However, the molecular mechanisms of its action are elusive.

Publication Title

A systematic assessment of chemical, genetic, and epigenetic factors influencing the activity of anticancer drug KP1019 (FFC14A).

Alternate Accession IDs

E-GEOD-76985

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE75447
Comparative transcriptome analysis of basal gene expression in Wild-type and Sen1N mutant of Saccharomyces cerevisiae
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

In Saccharomyces cerevisiae, Sen1 is a 252-kDa, nuclear superfamily-1 RNA/DNA helicase that encoded by an essential gene SEN1 (Senataxin). It is an important component of the Nrd1p-Nab3p-Sen1p (NRD1) complex that regulates the transcriptional termination of most non-coding and some coding transcripts at RNA polymerase pause sites. Sen1 specifically interacts with Rnt1p (RNase III), an endoribonuclease, and with Rpb1p (Rpo21p), a subunit of RNA polymerase II, through its N-terminal domain (NTD), which is a critical element of the RNA-processing machinery. Moreover, mutations in the N-terminal tail of SETX, a human ortholog of yeast Senataxin (Sen1) reported in neurological disorders.

Publication Title

Sen1, the homolog of human Senataxin, is critical for cell survival through regulation of redox homeostasis, mitochondrial function, and the TOR pathway in Saccharomyces cerevisiae.

Alternate Accession IDs

E-GEOD-75447

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE147516
Role of TGF-β signaling in hypoxia-induced alternative splicing in breast cancer cells
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Analysis of transcriptome post hypoxia and TGF-β treatment in breast cancer

Publication Title

Hypoxia-induced TGF-β-RBFOX2-ESRP1 axis regulates human MENA alternative splicing and promotes EMT in breast cancer.

Alternate Accession IDs

E-GEOD-147516

Sample Metadata Fields

Sex, Specimen part, Cell line

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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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