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accession-icon GSE70433
Gene expression in human or mouse brain with iron loading
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina MouseRef-8 v2.0 expression beadchip, Illumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Brain iron accumulation affects myelin-related molecular systems implicated in a rare neurogenetic disease family with neuropsychiatric features.

Sample Metadata Fields

Sex, Age, Specimen part, Disease

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accession-icon GSE70430
Substantia nigra (SN) and basal ganglia (BG) gene expression in neurodegenertion with brain iron accumulation (NBIA) cases vs normal controls
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

Differential gene expression is assessed in substantia nigra and basal ganglia of neurodegenertion with brain iron accumulation cases (BIA) compared to matched normal controls (c).

Publication Title

Brain iron accumulation affects myelin-related molecular systems implicated in a rare neurogenetic disease family with neuropsychiatric features.

Sample Metadata Fields

Sex, Age, Specimen part, Disease

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accession-icon GSE56549
Perception of fight outcome is needed to activate socially driven changes in brain transcriptome
  • organism-icon Danio rerio
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

Group living animals must be able to express different behavior profiles depending on their social status. This implies that the same genotype may translate into different behavioral phenotypes through socially driven differential gene expression. Here we show for the first time that what triggers the switch between status-specific neurogenomic states is not the objective structure of the social interaction but rather the subjects perception of its outcome. For this purpose we had male zebrafish fight either a real opponent or their own image on a mirror. Massive changes in the brain transcriptome were observed in real opponent fighters, which experience either a victory or a defeat. In contrast, mirror fighters, which had no information on fight outcome despite expressing aggressive behavior, failed to activate a neurogenomic response. These results indicate that, even in cognitively simple organisms such as zebrafish, neurogenomic responses underlying changes in social status rely on cognitive appraisal.

Publication Title

Assessment of fight outcome is needed to activate socially driven transcriptional changes in the zebrafish brain.

Sample Metadata Fields

Specimen part

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accession-icon GSE32540
Identification of novel tissue-specific transcription arising from E-cadherin/CDH1 intron2: a novel protein isoform increases gastric cancer cell invasion and angiogenesis.
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

E-cadherin, a protein encoded by the CDH1 gene is the dominant epithelial cell adhesion molecule playing a crucial role in epithelial tissue polarity and structural integrity. The progression of 90% or more carcinomas is believed to be mediated by disruption of normal E-cadherin expression, subcellular localization or function. Despite the strong correlation between E-cadherin loss and malignancy the mechanism through how this occurs is not known in most sporadic and hereditary epithelial carcinomas. Previous works have shown the importance of CDH1 intron 2 sequences for proper gene and protein expression supporting the possibility of these being cis-modulators of E-cadherin expression/function. but when co-expressed it led to reduced cell-cell adhesiveness, increased invasion and angiogenesis. By expression array analysis, IFITM1 and IFI27 levels were found to be increased upon CDH1a overexpression. Importantly, CDH1a was found to be de novo expressed in gastric cancer cell lines when compared to normal stomach.

Publication Title

Transcription initiation arising from E-cadherin/CDH1 intron2: a novel protein isoform that increases gastric cancer cell invasion and angiogenesis.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE57999
Expression data from baseline and post-endurance training in human PBMCs
  • organism-icon Homo sapiens
  • sample-icon 26 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

There is an association between transcriptome and the exercise-related phenotype. Peripheral blood cells suffer alterations in the gene expression pattern in response to perturbations caused by exercise. The acute response to endurance activates stress and inflammation, as well as growth and tissue repair responses.

Publication Title

PBMCs express a transcriptome signature predictor of oxygen uptake responsiveness to endurance exercise training in men.

Sample Metadata Fields

Sex, Specimen part, Disease, Disease stage, Treatment, Subject, Time

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accession-icon E-MEXP-2354
Transcription profiling by array of Saccharomyces cerevisiae overexpressing Gis1 after treatment with doxycycline
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome S98 Array (ygs98)

Description

The change of genome-wide transcription profiles as a result of Gis1 overexpression is monitored by comparing the transcriptomes isolated from cells where Gis1 overexpression is switched on or off. GIS1 was cloned into pCM190 vector under the control of the tetO7 promoter. The promoter is switched on when there is no doxycycline but off with doxycycline (20ug/ml). Cells were grown in medium with doxycycline, harvested, washes twice in sterile water, resuspended in the same medium with doxycycline (Dox+) or without doxycycline (dox-) and grown for additional 6 hours. Samples were taken for each condition at 3 and 6 hours. Time 0 sample was taken before resuspension.

Publication Title

The transcription activity of Gis1 is negatively modulated by proteasome-mediated limited proteolysis.

Sample Metadata Fields

Subject, Compound, Time

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accession-icon SRP026258
Zea mays cultivar:Nathan Transcriptome or Gene expression
  • organism-icon Zea mays
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

In order to characterize defense responses not only cytologically, but also on the transcript level, genome-wide sequencing of mRNA isolated from non-infected control leaves and from leaves inoculated either with the WT or with GLS1 overexpressing strains was performed, using Illumina Next Generation Sequencing Technology. In order to identify transcripts specifically induced in leaves infected by ß-1,3-glucan-exposing strains, transcript patterns of leaves inoculated with GLS1 overexpressing PtrpC:GLS1 strains were compared with those of the WT. In PtrpC:GLS1-inoculated leaves, a total of 2179 genes were more than 2.5-fold increased, with many genes known as genes typically up-regulated in PAMP-triggered defense responses. These genes include genes encoding PR proteins enzymes involved in cell wall re-inforcemen, and terpene synthases possibly involved in phytoalexin synthesis. Furthermore, increased transcript abundance of genes encoding serine-threonine receptor-like kinases calmodulin, as well as zinc-finger and WRKY transcription factors have been identified. Other up-regulated genes encode proteins involved in protein degradation, i.e. proteases, ubiquitin ligases, as well as enzymes involved in synthesis of auxin or cytokinin phytohormones. In comparison, 2164 genes were more than 2.5-fold down-regulated in maize leaves infected by PtrpC:GLS1 strains, as compared to WT-infected leaves. Several of the encoded proteins are known susceptibility factors. Forty-six down-regulated genes code for proteins containing iron or manganese, or are involved in uptake of these ions, suggesting major re-arrangement of the redox-status in maize leaves after ß-glucan perception. Overall design: Examination of plant defense responses in maize plants inoculated with 2 different Colletotrichum graminicola strains.

Publication Title

Infection structure-specific expression of β-1,3-glucan synthase is essential for pathogenicity of Colletotrichum graminicola and evasion of β-glucan-triggered immunity in maize.

Sample Metadata Fields

Age, Subject, Time

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accession-icon GSE140213
A class II-restricted chlamydia-specific CD8ɣ13 T cell clone protects the genital tract during Chlamydia muridarum infection
  • organism-icon Mus musculus
  • sample-icon 38 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

The T cell response to Chlamydia genital tract infections in humans and mice is unusual in that the majority of antigen-specific CD8 T cells are not restricted by HLA/MHC class I and therefore have been referred to as “unrestricted” or “atypical”.   We previously reported that a subset of unrestricted murine Chlamydia-specific CD8 T cells had an unusual cytokine polarization pattern that included IFN-ɣ and IL-13.  For this report, we investigated the transcriptome of Chlamydia-specific CD8ɣ13 T cells, comparing them to Chlamydia-specific multifunctional Tc1 clones using gene expression micro array analysis.  The molecular study revealed that CD8ɣ13 polarization included IL-5 in addition to IFN-γ and IL-13.  Adoptive transfer studies were performed with Tc1 clone and CD8ɣ13 T cell clones to determine whether either influenced bacterial clearance or immunopathology during Chlamydia muridarum (Cm) genital tract infections.  To our surprise, an adoptively transferred CD8ɣ13 T cell clone was remarkably proficient at preventing chlamydia immunopathology while the multifunctional Tc1 clone did not enhance clearance or significantly protect from immunopathology.  Mapping studies with MHC class I- and class II-deficient splenocytes showed our previously published Chlamydia-specific CD8 T cell clones are MHC class II-restricted.   MHC class II-restricted CD8 T cells may play important roles in protection from intracellular pathogens that limit class I antigen presentation or deplete the CD4 T cell compartment.

Publication Title

A Class II-Restricted CD8γ13 T-Cell Clone Protects During Chlamydia muridarum Genital Tract Infection.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP081284
Cell responses to dysregulated VZV-induced cell-cell fusion
  • organism-icon Homo sapiens
  • sample-icon 26 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The highly conserved herpesvirus glycoprotein complex, gB/gH-gL, mediates membrane fusion during virion entry and cell-cell fusion. Varicella-zoster virus (VZV) characteristically forms multi-nucleated cells, or syncytia, during the infection of human tissues but little is known about this process. The cytoplasmic domain of VZV gB (gBcyt) has been implicated in cell-cell fusion regulation because a gB[Y881F] substitution causes hyperfusion. The gBcyt regulation is necessary for VZV pathogenesis as the hyperfusogenic mutant gB[Y881F] is severely attenuated in human skin xenografts. In this study, gBcyt regulated fusion was investigated by comparing melanoma cells infected with wild type-like VZV or hyperfusogenic mutants. The gB[Y881F] mutant exhibited dramatically accelerated syncytia formation in melanoma cells caused by fusion of infected cells with many uninfected cells, increased cytoskeleton reorganization and rapid displacement of nuclei to dense central structures when compared to pOka using live cell confocal microscopy. VZV and human transcriptomes were concurrently investigated using RNA-seq to identify viral and cellular responses induced when the gBcyt regulation was disrupted by the gB[Y881F] substitution. The expression of four vital VZV genes, ORF61 and glycoproteins, gC, gE and gI, was significantly reduced at 36 hours post infection for the hyperfusogenic mutants. Importantly, hierarchical clustering demonstrated an association of differential gene expression with dysregulated gBcyt-mediated fusion. A subset of Ras GTPase genes linked to membrane remodeling were upregulated in cells infected with the hyperfusogenic mutants. These data implicate the gBcyt in the regulation gB fusion function that, if unmodulated, triggers cellular processes leading to hyperfusion that attenuates VZV infection. Overall design: Biological duplicates from 3 time points (12, 24 and 36 hours post infection) of uninfected MeWo cells or MeWo cells infected with varicella-zoster virus strain pOka or mutants gB[Y881F], gB[Y920F] or gB[Y881/920F]

Publication Title

Dysregulated Glycoprotein B-Mediated Cell-Cell Fusion Disrupts Varicella-Zoster Virus and Host Gene Transcription during Infection.

Sample Metadata Fields

Cell line, Subject, Time

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accession-icon GSE69719
Brain transcriptomic response to social eavesdropping in zebrafish
  • organism-icon Danio rerio
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon Affymetrix Genechip Zebrafish ST Genome Array 1.1 (zebgene11st)

Description

Public information is widely available at low cost to animals living in social groups. For instance, bystanders may eavesdrop on signaling interactions between conspecifics and use it to adapt their subsequent behavior towards the observed individuals. This social eavesdropping ability is expected to require specialized mechanisms such as social attention, which selects social information available for learning. To begin exploring the genetic basis of social eavesdropping, we used a previously established attention paradigm in the lab to study the brain gene expression profile of male zebrafish in relation to the attention they have paid towards conspecifics involved or not involved in agonistic interactions. Microarray gene chips were used to characterize their brain transcriptomes based on differential expression of single genes and gene sets. These analyses were complemented by promoter region-based techniques. Using data from both approaches, we further drafted protein interaction networks. Our results suggest that attentiveness towards conspecifics, whether interacting or not, activates pathways linked to neuronal plasticity and memory formation. The network analyses suggested that fos and jun are key players on this response, and that npas4a, nr4a1 and egr4 may also play an important role.

Publication Title

Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio).

Sample Metadata Fields

Sex, Specimen part, Treatment

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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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