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accession-icon GSE21651
Differential expression for salt and drought stress
  • organism-icon Oryza sativa
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Leaf samples were used. We exposed young seedlings to NaCl and drought.

Publication Title

Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks.

Sample Metadata Fields

Specimen part

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accession-icon GSE109283
Expression data of OsSHMT Arabidopsis
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Plants were exposed to NaCl (150mM) stress for 24 hours

Publication Title

Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice Confers Tolerance to Salinity Stress in <i>E. coli</i> and Arabidopsis.

Sample Metadata Fields

Age

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accession-icon GSE5167
Rice seedling hormone treatment
  • organism-icon Oryza sativa
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Indica rice seedlings of IR64 variety were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark. Seedlings were incubated in 0.1% dimethyl sulfoxide (control) or 50 micromolar solutions of indole-3-acetic acid (IAA treatment) and benzyl aminopurine (BAP treatment) for 1h and 3h. Equal amounts of 1h and 3h samoles were pooled for each treatment before RNA isolation. The 5 micrograms of each total RNA sample was processed for microarray analysis according to Affymetrix protocol.

Publication Title

Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice.

Sample Metadata Fields

Specimen part

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accession-icon GSE6858
Expression data from experimental murine asthma
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Experimental asthma was induced in BALB/c mice by sensitization and challenge with the allergen ovalbumin. Control groups received PBS. To investigate the innate immune component of experimental asthma, we also analyzed recombinase activating gene (RAG) deficient mice following exposure to ovalbumin and control PBS

Publication Title

Hubs in biological interaction networks exhibit low changes in expression in experimental asthma.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE37557
Gene expression analysis in response to various hormone treatments
  • organism-icon Oryza sativa
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Hormones effect various plant developmental processes by altering gene expression. The expression of several genes is regulated by plant hormones and many of these genes are regulated commonly and specifically by various hormones.

Publication Title

Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice.

Sample Metadata Fields

Specimen part

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accession-icon GSE41963
Gene expression analysis in wild-type and OsGRX8 overexpression line in response to various treatments
  • organism-icon Arabidopsis thaliana
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Glutaredoxins (GRXs) are the ubiquitous oxidoreductase enzymes, which play important role in defense against various stresses. To analyze the function of a CC-type rice GRX gene, OsGRX8, we overexpressed it into Arabidopsis constitutively. The physiological analyses revealed that overexpression of GRX gene enhanced abiotic stress tolerance in transgenic plants as compared to wild-type.

Publication Title

Modified expression of an auxin-responsive rice CC-type glutaredoxin gene affects multiple abiotic stress responses.

Sample Metadata Fields

Specimen part

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accession-icon GSE79212
Gene expression analysis in wild-type and OsHOX24 rice overexpression line under control and drought stress conditions
  • organism-icon Oryza sativa
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice (US) Gene 1.0 ST Array (rusgene10st)

Description

Several homeobox genes belonging to HD-ZIP I subfamily are highly induced by drought stress at various developmental stages in rice. To analyze the role of a candidate HD-ZIP I subfamily member, OsHOX24, we constitutively overexpressed it in rice. The physiological analyses revealed that overexpression of OsHOX24 gene reduced drought stress tolerance in transgenic plants as compared to wild-type.

Publication Title

Over-Expression of <i>OsHOX24</i> Confers Enhanced Susceptibility to Abiotic Stresses in Transgenic Rice via Modulating Stress-Responsive Gene Expression.

Sample Metadata Fields

Specimen part

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accession-icon GSE5465
Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

10-day-old wild-type and homozygous transgenic Arabidopsis seedlings (overexpressing OsTOP6A3 and OsTOP6B) grown under normal growth conditions were used for total RNA isolation. The 5 micrograms of each total RNA sample was processed for microarray analysis according to Affymetrix protocol.

Publication Title

Overexpression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants.

Sample Metadata Fields

Specimen part

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accession-icon GSE6812
Gene expression in wild-type and transgenic plants overexpressing rice OsTOP6A1 gene
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

10-day-old wild-type and homozygous transgenic Arabidopsis seedlings (overexpressing rice topoisomerase 6 subunit A1; OsTOP6A1) grown under normal growth conditions were used for total RNA isolation. The 5 micrograms of each total RNA sample was processed for microarray analysis according to Affymetrix protocol.

Publication Title

Constitutive expression of a meiotic recombination protein gene homolog, OsTOP6A1, from rice confers abiotic stress tolerance in transgenic Arabidopsis plants.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE79188
Gene expression analysis in wild-type and OsHOX24 Arabidopsis overexpression line
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Homeobox transcription factors are known to regulate plant growth and development. Recently, they have also been implicated in abiotic stress responses. To analyze the role of HD-ZIP I subfamily member, OsHOX24, we constitutively overexpressed it in Arabidopsis. The physiological analyses revealed that overexpression of OsHOX24 gene severely reduced abiotic stress tolerance in transgenic plants as compared to wild-type.

Publication Title

Characterization of Rice Homeobox Genes, OsHOX22 and OsHOX24, and Over-expression of OsHOX24 in Transgenic Arabidopsis Suggest Their Role in Abiotic Stress Response.

Sample Metadata Fields

Age, Specimen part

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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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