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accession-icon GSE81666
Expression data of nuclear mRNA export mutant rae1-167 cells
  • organism-icon Schizosaccharomyces pombe
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

rae1 is an essential gene and encodes one of nuclear pore complex. rae1-167 mutant cells show rapid accumulation of polyA-RNA in the nucleus at 36C followed by protein accumulation, suggesting that accumulated nuclear mRNA influences nucelar cytooplasmic transport.

Publication Title

A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control.

Sample Metadata Fields

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accession-icon GSE66685
Expression data from mutant of RSC chromatin-remodeling complex in respiratory growth
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

RSC is a growth essential ATP-dependent chromatin-remodeling complex of Saccharomyces cerevisiae. Nps1/Sth1 is the ATPase subunit of the complex. A temperature-sensitive mutant allele of NPS1, nps1-13 and the null mutation of the RSC2 or RSC7 gene showed growth defect on a medium containing non fermentable carbon source, such as lactate or ethanol-glycerol (YPEG), suggested a possibility that RSC plays a role on mitochondria function.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE76206
Expression data from SSG1 long-lived mutant
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

The SSG1-1 mutation was an allele of the YHR032W gene in Saccharomyces cerevisiae. The SSG1-1 mutants contained higher levels of AdoMet than wild type (WT). SSG1-1 single mutants were shown to have a long lifespan, suggesting that the Ssg1-1 protein might have a role in longevity.

Publication Title

Stimulating S-adenosyl-l-methionine synthesis extends lifespan via activation of AMPK.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE36228
Affymetrix Cotton Genome array expression data of cotton fiber at different developmental stages from different varieties of Gossypium hirsutum
  • organism-icon Gossypium hirsutum
  • sample-icon 89 Downloadable Samples
  • Technology Badge Icon Affymetrix Cotton Genome Array (cotton)

Description

Cotton fiber were used for the expression analysis at different developmental stages

Publication Title

Transcriptome dynamics during fibre development in contrasting genotypes of Gossypium hirsutum L.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE45690
Functional characterization of Taf4b in Arabidopsis thaliana
  • organism-icon Arabidopsis thaliana
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Expression analysis was performed with two TDNA insertion mutants of taf4b i.e; taf4bprm (TDNA insertion in promoter region) and taf4bint (TDNA insertion in intronic region), Taf4b overexpression lines, taf4bprmcpr5 double mutant lines (Double mutant was generated by crossing taf4bprm with cpr5) and Col-0 in normal condition as well as with taf4bprm mutant and Col-0 infected with fungi AB (Alternaria brassicicola) and bacteria ES4 (Pseudomonas syringae pv.maculicola ES4326 ) in different perspectives.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE53564
Effect of As (V) 50m in transcription change of six rice genotypes (BRG-12, BRG-15, BRG-20, CN1646-5, NAYANMONI and CN1646-2)
  • organism-icon Oryza sativa indica group
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Affymetrix expression analysis was used to check transcipt expression in As (V) stress.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE4295
Sugar stress during fermentation (baker's yeast)
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 27 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

Functional genomic analysis using different types of baker's yeast.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE40061
Role of CAMTA1 gene under drought stress
  • organism-icon Arabidopsis thaliana
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

The CAMTA1 mutant and Col-0 were studied under water and drought condition. The camta1 showed stunted primary root growth under osmotic stress. The expression analysis revealed drought recovery as major indicative pathway along with membrane and chloroplast related protein in camta1 under drought stress. Large number of positively regulated genes were related to osmotic balance, transporters, AP2 and ABA. We used Affymetrix expression analysis to validate the role of CAMTA1 under drought stress.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE33276
Gene expression profiles of S. cerevisiae under heat stress
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

Genes whose expression correlated to the degree of thermotolerance in S. cerevisiae were identified by DNA microarray analysis.

Publication Title

Identification of a gene, FMP21, whose expression levels are involved in thermotolerance in Saccharomyces cerevisiae.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE15461
Insufficiency of Copper Ion Homeostasis Causes Freeze-Thaw Injury of Yeast Cells
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury.

Publication Title

Insufficiency of copper ion homeostasis causes freeze-thaw injury of yeast cells as revealed by indirect gene expression analysis.

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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