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accession-icon GSE629
Auxin-mediated gene expression in WT, iaa17, axr3 and iaa5iaa6iaa19 mutants
  • organism-icon Arabidopsis thaliana
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5M IAA) for 2 h. Columbia (WT), IAA17 loss of function mutant allele (iaa17-2), IAA17 gain of function mutant allele (axr3-1) and iaa5 iaa6 iaa19 triple loss of function mutant allele (i5i6i19) were used for this study. Each experimental condition has three true replicates for a total of 24 hybridizations. Data

Publication Title

Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE627
Auxin mediated gene expression in WT, arf7, arf19 and arf7 arf19 mutants
  • organism-icon Arabidopsis thaliana
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

RNA samples were extracted from liquid cultured seedlings treated with or without auxin (5M IAA) for 2 h.

Publication Title

Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE42896
Expression data from Arabidopsis seedlings upon LRIS using NAA (1-Naphthaleneacetic acid) or non-auxin-like lateral root inducer naxillin
  • organism-icon Arabidopsis thaliana
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture. To further explore the specificity of naxillin for lateral root development, we compared the early effects of naxillin at the transcriptome level with NAA (1-Naphthaleneacetic acid) in roots of 3-day-old seedlings after 2-h and 6-h treatment.

Publication Title

A role for the root cap in root branching revealed by the non-auxin probe naxillin.

Sample Metadata Fields

Age, Specimen part, Treatment

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accession-icon E-MEXP-2912
Transcription profiling by array of different organism parts of Arabidopsis mutant for arf7 and arf19
  • organism-icon Arabidopsis thaliana
  • sample-icon 30 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Arabidopsis seedlings, of both wild-type and an ARF7/ARF19 double knockout mutant, were grown to 7 days post-germination. The roots were then dissected into 5 developmental zones, the meristem, early elongation zone, late elongation zone, mature root and lateral root zone. The sections then underwent transcriptional profiling to identify processes and regulatory events specific and in common to the zones.

Publication Title

A novel aux/IAA28 signaling cascade activates GATA23-dependent specification of lateral root founder cell identity.

Sample Metadata Fields

Age, Specimen part

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accession-icon SRP094587
Characterization of meningeal type 2 innate lymphocytes and their response to CNS injury
  • organism-icon Mus musculus
  • sample-icon 53 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

The meningeal space is occupied by a diverse repertoire of innate and adaptive immune cells. CNS injury elicits a rapid immune response that affects neuronal survival and recovery, but the role of meningeal inflammation in CNS injury remains poorly understood. Here we describe group 2 innate lymphoid cells (ILC2s) as a novel cell type resident in the healthy meninges that is activated following CNS injury. ILC2s are present throughout the naïve mouse meninges, though are concentrated around the dural sinuses, and have a unique transcriptional profile relative to lung ILC2s. After spinal cord injury, meningeal ILC2s are activated in an IL-33 dependent manner, producing type 2 cytokines. Using RNAseq, we characterized the gene programs that underlie the ILC2 activation state. Finally, addition of wild type lung-derived ILC2s into the meningeal space of IL-33R-/- animals improves recovery following spinal cord injury. These data characterize ILC2s as a novel meningeal cell type that responds to and functionally affects outcome after spinal cord injury, and could lead to new therapeutic insights for CNS injury or other neuroinflammatory conditions. Overall design: ILC2s were isolated from 10 week C57/Bl6 mice with and without spinal cord injury (1 day post injury). 5 mice were pooled per group, with meninges dissected, digested, and FACs sorted (CD45+/DAPI-/Lin–/St2+/Thy1+) directly into RNA lysis buffer.

Publication Title

Characterization of meningeal type 2 innate lymphocytes and their response to CNS injury.

Sample Metadata Fields

Age, Specimen part, Cell line, Subject

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accession-icon SRP127628
Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia [LPS]
  • organism-icon Mus musculus
  • sample-icon 48 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Peripherally derived macrophages infiltrate the brain after bone marrow transplantation and during central nervous system (CNS) inflammation. It was initially suggested that these engrafting cells were newly derived microglia and that irradiation was essential for engraftment to occur. However, it remains unclear whether brain-engrafting macrophages (beMfs) acquire a unique phenotype in the brain, whether long-term engraftment may occur without irradiation, and whether brain function is affected by the engrafted cells. In this study, we demonstrate that chronic, partial microglia depletion is sufficient for beMfs to populate the niche and that the presence of beMfs does not alter behavior. Furthermore, beMfs maintain a unique functional and transcriptional identity as compared with microglia. Overall, this study establishes beMfs as a unique CNS cell type and demonstrates that therapeutic engraftment of beMfs may be possible with irradiation-free conditioning regimens. Overall design: Microglia were isolated from the brains of adult male c57BL/6 mice given bone marrow tranplants (BMT) with or without head shield. All mice received PLX5622 for 2 weeks, then placed and normal chow to recoever. Some mice were then challenged with LPS. Cells were isolated by MACS using CD11b magnetic beads.

Publication Title

Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia.

Sample Metadata Fields

Age, Specimen part, Cell line, Treatment, Subject

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accession-icon SRP079704
Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Peripherally derived macrophages infiltrate the brain after bone marrow transplantation and during central nervous system (CNS) inflammation. It was initially suggested that these engrafting cells were newly derived microglia and that irradiation was essential for engraftment to occur. However, it remains unclear whether brain-engrafting macrophages (beMfs) acquire a unique phenotype in the brain, whether long-term engraftment may occur without irradiation, and whether brain function is affected by the engrafted cells. In this study, we demonstrate that chronic, partial microglia depletion is sufficient for beMfs to populate the niche and that the presence of beMfs does not alter behavior. Furthermore, beMfs maintain a unique functional and transcriptional identity as compared with microglia. Overall, this study establishes beMfs as a unique CNS cell type and demonstrates that therapeutic engraftment of beMfs may be possible with irradiation-free conditioning regimens. Overall design: Mice were given 1000rad whole body irradiation, followed by bone marrow transplant with UBC-GFP bone marrow at 8 weeks of age. Engraftment was allowed to occur for 8 months, then engrafting macrophages and microglia were isolated from whole brains for RNA-Seq.

Publication Title

Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia.

Sample Metadata Fields

Age, Specimen part, Cell line, Subject

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accession-icon GSE82094
Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE11259
Role of epithelial to mesenchymal transition (EMT) in spontaneous breast cancer metastasis
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Epithelial-mesenchymal transition (EMT) has been linked to cancer progression and metastatic propensity. The 4T1 tumor is a clinically relevant model of spontaneous breast cancer metastasis. Here we characterize 4T1-derived cell lines for EMT, in vitro invasiveness and in vivo metastatic ability. Contrary to expectations, the 67NR cells, which form primary tumors but fail to metastasize, express vimentin and N-cadherin, but not E-cadherin. 4T1 cells, however, express E-cadherin, are highly migratory and invasive, and metastasize to multiple sites. The 66cl4 metastatic cells display mixed epithelial and mesenchymal markers, but are less migratory and invasive than 67NR cells. These findings demonstrate that the metastatic ability of breast cancer cells does not correlate with genotypic and phenotypic properties of EMT per se, and suggest that other processes may govern metastatic capability. Gene expression analysis also has not identified differences in EMT markers, but has identified several candidate genes that may influence metastatic ability.

Publication Title

Epithelial-mesenchymal transition (EMT) is not sufficient for spontaneous murine breast cancer metastasis.

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon GSE82092
Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light (3h time point)
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

Photobiomodulation (PBM) with blue light induces a biphasic dose response curve in proliferation of immortalized human keratinocytes (HaCaT), with a maximum anti-proliferative effect reached with 30min (41.4J/cm). The aim of this study was to test the photobiomodulatory effect of 41.4J/cm2 blue light irradiation on ROS production, apoptosis and gene expression at different time points after irradiation of HaCaT cells in vitro. ROS concentration was increased 30min after irradiation. However, already 1h after irradiation, cells were able to reduce ROS and balance the concentration to a normal level. The sudden increase in ROS did not damage the cells, which was demonstrated with FACS analysis where HaCaT cells did not show any sign of apoptosis after blue light irradiation. Furthermore, a time course could be seen in gene expression analysis after blue light, with an early response of stimulated genes already 1h after blue light irradiation, leading to the discovery of the aryl hydrocarbon receptor as possible target for blue light irradiation.

Publication Title

Gene expression profiling reveals aryl hydrocarbon receptor as a possible target for photobiomodulation when using blue light.

Sample Metadata Fields

No 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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