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accession-icon GSE155640
Expression data from THP1-wt and THP1-NTR+ cells with LSD1 inhibitor (OG86), Nitroreductase NfsB (NTR) prodrug and negative control
  • organism-icon Homo sapiens
  • sample-icon 42 Downloadable Samples
  • Technology Badge Icon Affymetrix Clariom S Human array (clariomshuman)

Description

The Nitroreductase NfsB (NTR) prodrug of an LSD1 inhibitor is inactive in wild-type THP1 cells, but the prodrug gets activated in the LSD1 inhibitor by the NTR in NTR-expressing THP1 cells (THP1-NTR+).

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Cell line, Treatment

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accession-icon GSE90954
Effect of TGFb treatment (1 ng/ml) on gene expression in Hepa1-6 cells
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The goal of the study is a high-throughput evaluation of the effect of TGFb treatment on gene expression.

Publication Title

Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression.

Sample Metadata Fields

Specimen part

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accession-icon GSE90513
Neuronal activity, TGF signaling and unpredictable chronic stress affect transcription of Gadd45 family members in vitro and in vivo
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE90508
Neuronal activity, TGF signaling and unpredictable chronic stress affect transcription of Gadd45 family members in vitro and in vivo [Affymetrix]
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Neuronal activity is altered in several neurological and psychiatric diseases. Upon depolarization not only neurotransmitters are released but also cytokines and other activators of signaling cascades. Unraveling their complex implication in transcriptional control in receiving cells will contribute to understand specific central nervous system (CNS) pathologies and will be of therapeutical interest. In this study we depolarized mature hippocampal neurons in vitro using KCl and revealed increased release not only of Brain-derived neurotrophic factor (BDNF), but also of Transforming growth factor beta (TGFB). Neuronal activity together with BDNF and TGFB controls transcription of DNA modifying enzymes specifically members of the DNA-damage-inducible (Gadd) family, Gadd45a, Gadd45b, and Gadd45g. MeDIP followed by massive parallel sequencing and transcriptome analyses revealed less DNA methylation upon KCl treatment. Thereby, psychiatric disorder-related genes, namely Tshz1, Foxn3, Jarid2, Per1, Map3k5, and Arc are transcriptionally activated and demethylated upon neuronal activation. To analyze whether misexpression of Gadd45 family members can be associated with psychiatric diseases, we applied unpredictable chronic mild stress (UCMS) as established model for depression to mice.UCMS lead to a reduced expression of Gadd45 family members. Taken together, our data demonstrate that Gadd45 family members are new putative targets for UCMS treatments.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE17667
Pou5f1 transcription targets in zebrafish
  • organism-icon Danio rerio
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development.

Sample Metadata Fields

No sample metadata fields

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accession-icon E-MEXP-1957
Transcription profiling of Arabodpsis seedings exposed to UV-B irradiation
  • organism-icon Arabidopsis thaliana
  • sample-icon 36 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Interaction of COP1 and UVR8, which regulate UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis thaliana

Publication Title

Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis.

Sample Metadata Fields

Age, Treatment, Time

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accession-icon GSE13109
Effect of hypoxia on gene expression in Grey poplar
  • organism-icon Populus tremula x populus alba
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Poplar Genome Array (poplar)

Description

The molecular responses of Grey poplar (Populus x canescens) following root hypoxia were studied in roots and leaves using transcript profiling. Grey poplar is a flooding tolerant tree species and analysis of the molecular response to hypoxia may indicate possible adaptation mechanisms to this stress.

Publication Title

Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE28446
Expression data from Arabidopsis mature siliques
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Analysis of the transcriptomes of nearly ripe siliques (18-19 DAP) of the rdo2-1, rdo3 and hub1-2 (rdo4) mutants in comparison with wild-type Ler, using Affymetrix GeneChip Arabidopsis ATH1 Genome Array.

Publication Title

Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role for the polymerase associated factor 1 complex in seed dormancy.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE17657
Experiment 4: Affymetrix validation array
  • organism-icon Danio rerio
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

Zebrafish embryo were analyzed at 30 and 60 % epiboly for changes in transcriptome of wild-type and MTspg mutant embryos

Publication Title

Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE50786
Comparison of histone deacetylase 9-1 mutant (SALK_001723) dry seed transcriptome with Col wild-type
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Analysis of the transcriptome of dry hda9-1 mutant seeds with those of Col wild-type seeds, using Affymetrix GeneChip Arabidopsis ATH1 Genome Array.

Publication Title

HISTONE DEACETYLASE 9 represses seedling traits in Arabidopsis thaliana dry seeds.

Sample Metadata Fields

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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