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accession-icon GSE17099
Effect of AtHRE1 and AtHRE2 overexpression in normoxia and hypoxia
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

HRE1 and HRE2 are two ERF transcription factors induced by low oxygen. In this work we analyzed the effect of ectopic expression of HRE1 and HRE2 on the arabidopsis transcriptome in aerobic and hypoxic (1% O2) conditions. While HRE1 has a moderate effect on the expression of anaerobic genes under hypoxia, HRE2 does not affect them either under aerobic or hypoxic conditions.

Publication Title

HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana.

Sample Metadata Fields

Age, Treatment

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accession-icon GSE11558
transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
  • organism-icon Arabidopsis thaliana
  • sample-icon 27 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

- Background and Aims: Oxygen can fall to low concentrations within plant tissues, either because of environmental factors that decrease the external oxygen concentration or because the movement of oxygen through the plant tissues cannot keep pace with the rate of oxygen consumption. Recent studies document that plants can decrease their oxygen consumption in response to relative small changes in oxygen concentrations to avoid internal anoxia. The molecular mechanisms underlying this response have not been identified yet. The aim of this study was to use transcript and metabolite profiling to investigate the genomic response of Arabidopsis roots to a mild decrease in oxygen concentrations.

Publication Title

Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP102698
Response of Arabidopsis thaliana seedlings to acyl-CoAs
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

Floodings already have a nearly 60% share in the worldwide damage to crops provoked by natural disasters. Climate change will cause plants to be even more frequently exposed to oxygen limiting conditions (hypoxia) in the near future due to heavy precipitation and concomitant waterlogging or flooding events in large areas of the world. Although the homeostatic regulation of adaptive responses to low oxygen stress in plants is well described, it remained unknown by which initial trigger the molecular response to low-oxygen stress is activated. Here, we show that a hypoxia-induced decline of the ATP level of the cell reduces LONG-CHAIN ACYL-COA SYNTHETASE (LACS) activity, which leads to a shift in the composition of the acyl-CoA pool. High oleoyl-CoA levels release the transcription factor RELATED TO APETALA 2.12 (RAP2.12) from its interaction partner ACYL-COA BINDING PROTEIN (ACBP) at the plasma membrane to induce low oxygen-specific gene expression. We show that different acyl-CoAs provoke unique molecular responses revealing a novel role as cellular signalling component also in plants. In terms of hypoxia signalling, dynamic acyl-CoA levels integrate the cellular energy status into the oxygen signalling cascade with ACBP and RAP2.12 being the central hub. The conserved nature of the ACBP:RAP2.12 module in crops and the novel mechanistic understanding of how low-oxygen stress responses are initiated by oleoyl-CoA in plants provide useful leads for enhancing future food security. Overall design: 1 control and 3 treatments with different forms of acyl-CoA in triplicate biological replicates

Publication Title

Low-oxygen response is triggered by an ATP-dependent shift in oleoyl-CoA in <i>Arabidopsis</i>.

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon GSE16749
miR-155 role in osteoclast differentiation
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

We used microarrays to understand the effect miR-155 has on osteoclast differentiation.

Publication Title

miRNA-based mechanism for the commitment of multipotent progenitors to a single cellular fate.

Sample Metadata Fields

Cell line

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accession-icon GSE48566
Expression data from mammary tumors from MOLF/Ei x PyMT mouse crosses and Diversity Outcross x PyMT mouse crosses
  • organism-icon Mus musculus
  • sample-icon 267 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Genetic background may contribute to PAM50 gene expression breast cancer subtype assignments.

Sample Metadata Fields

Specimen part

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accession-icon GSE48564
Expression data from mammary tumors from a MOLF/Ei x PyMT mouse cross
  • organism-icon Mus musculus
  • sample-icon 134 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Mouse genetic crosses were established between the PyMT model of metastatic breast cancer and MOLF/Ei strain. Tumors were harvested from the animals for gene expression analysis to identify genes associated with progression to distant metastatic disease.

Publication Title

Genetic background may contribute to PAM50 gene expression breast cancer subtype assignments.

Sample Metadata Fields

Specimen part

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accession-icon GSE48565
Expression data from mammary tumors from a Diversity Outcross x PyMT mouse cross
  • organism-icon Mus musculus
  • sample-icon 133 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Mouse genetic crosses were established between the PyMT model of metastatic breast cancer and the G5 generation of the Diversity Outcross (DO). Tumors were harvested from the animals for gene expression analysis to identify genes associated with progression to distant metastatic disease.

Publication Title

Genetic background may contribute to PAM50 gene expression breast cancer subtype assignments.

Sample Metadata Fields

Specimen part

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accession-icon SRP120487
Trnascriptome analysis of HeLa cells infected with rTHOV-wt, -dML, -SW mutant or mock-treated
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

The goal of the study was to compare transcriptome changes in HeLa cells after infection with recombinant Thogoto virus (wild-type, ML deletioin mutant or ML SW mutant not able to interact wiith TFIIB. While wild-type virus is able to inhibit inflammatory genes, ML deletion mutant and TFIIB-non-interacting mutant lose this effect on gene transcription. Overall design: Examination of transcriptome changes in HeLa cells under steady state or after THOV infection using Illumina HiSeq.

Publication Title

Viral targeting of TFIIB impairs de novo polymerase II recruitment and affects antiviral immunity.

Sample Metadata Fields

Cell line, Subject

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accession-icon GSE33631
Expression data from mock treated/oxidized HF after 24h incubation with/without monocytes
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Cells are constantly exposed to stress. Most of those stresses do not necessarily cause cell death or visible damage. The present study explores the way the immune system responds to such sub lethal stressed cells.

Publication Title

Cells exposed to sublethal oxidative stress selectively attract monocytes/macrophages via scavenger receptors and MyD88-mediated signaling.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon SRP125118
Aged Hematopoietic Stem Cells Drive Aging-Associated Immune Remodeling
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Phenotypic and functional changes seen in the aged adaptive immune system are primarily driven by aging of hematopoietic stem cells (HSCs), pharmacological rejuvenated aged HSCs were able to reconstituted a youthful immune system Overall design: We employed RNA-seq to assess similarities/differences between naive CD4+ T cells and CD19+ B cells isolated from RAG1-/- recipients transplanted with either young, old or old rejuvenated (CASIN treated) HSCs

Publication Title

Aged murine hematopoietic stem cells drive aging-associated immune remodeling.

Sample Metadata Fields

Specimen part, Cell line, Subject

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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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