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GSE69340
Mus musculus
27 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We used microarrays of eight different cell types in cortex to conduct specificity index analysis for detailed cell type specific molecular profile.
Publication Title
Layer 2/3 pyramidal cells in the medial prefrontal cortex moderate stress induced depressive behaviors.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
GABAergic interneuron in the cortex comprise a very heterogenous group. and it is critical to identify discrete interneuron types to understand how their contributions to behavior can be modulated by external and internal cues. However, molecular difinition of these interneuron cell groups has been difficult. Comparative analysis of different interneuron subtypes can provide us new candidate marker genes which could target more specific interneuon cell group. Here we identify oxytocin responsive novel class of interneuron through our comparative analysis.
Publication Title
Oxytocin modulates female sociosexual behavior through a specific class of prefrontal cortical interneurons.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 3 Downloadable Samples
Illumina HiSeq 2000
Description
5-hydroxymethylcytosine (5hmC) occurs at maximal levels in postmitotic neurons where its accumulation is cell specific and correlated with gene expression. Here we demonstrate that the distribution of 5hmC in CG and non-CG dinucleotides is distinct, and that it reflects the binding specificity and genome occupancy of methylcytosine binding protein 2 (MeCP2). In expressed gene bodies, accumulation of 5hmCG acts in opposition to 5mCG resulting in “functional” demethylation and diminished MeCP2 binding, thus facilitating transcription. Non-CG hydroxymethylation occurs predominantly in CA dinucleotides (5hmCA) and it accumulates in regions flanking active enhancers. In these domains, oxidation of 5mCA to 5hmCA does not alter MeCP2 binding or expression of adjacent genes. We conclude that the role of 5-hydroxymethylcytosine in postmitotic neurons is to functionally demethylate expressed gene bodies while retaining the role of MeCP2 in chromatin organization. Overall design: Examination of genome wide cytosine methylation and hydroxymethylation per context in cerebellar granule cells and their function in MeCP2 binding. Nuclear RNA-Seq dataset.
Publication Title
5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
To investigate the role of CYP2B in lipid metabolism, a Cyp2b triple knockout mouse lacking Cyp2b9, Cyp2b10, and Cyp2b13 was developed using CRISPER/Cas9. Wildtype (WT) and Cyp2b-null mice were fed a normal diet (ND) or a 60% high-fat diet (HFD) for 10 weeks. RNA was extracted from the livers of male and female mice from all treatment groups and used for RNA seqencing. RNAseq data demonstrated that hepatic gene expression in ND-fed Cyp2b-null male mice is similar to HFD-fed WT mice, indicating that Cyp2b-null male mice are reacting as if they are receiving a HFD even if they are not. Gene ontology and KEGG pathways show perturbations in lipid metabolism pathways, including PUFA metabolism, fatty acid elongation, and glycerophospholipid metabolism. Overall design: Use RNA-sequencing to investigate the role of Cyp2b in hight-fat diet-induced obesity on a transcriptomic level, by comparing the livers of WT and Cyp2b-null mice fed a HFD for 10 weeks using Illumina technology.
Publication Title
Cyp2b-null male mice are susceptible to diet-induced obesity and perturbations in lipid homeostasis.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 49 Downloadable Samples
- NextSeq 500
Description
Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression events in specific cell types in a broad range of species. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping, quantitative PCR, and immunofluorescence localization. Studies of sixteen human postmortem brains revealed cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event experienced by three donors. Our data establish a comprehensive approach for analysis of unique molecular events associated with specific circuits and cell types in a wide variety of human conditions. Overall design: RNA purified from nuclei or cytoplasm from mouse, rat, or human cerebellum. ATAC-seq was also performed using cerebellar nuclei from the three species.
Publication Title
Species and cell-type properties of classically defined human and rodent neurons and glia.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples- Mus musculus
- 29 Downloadable Samples
- Illumina HiSeq 2500, NextSeq 500
Description
Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression events in specific cell types in a broad range of species. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping, quantitative PCR, and immunofluorescence localization. Studies of sixteen human postmortem brains revealed cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event experienced by three donors. Our data establish a comprehensive approach for analysis of unique molecular events associated with specific circuits and cell types in a wide variety of human conditions. Overall design: RNA purified from nuclei or cytoplasm from mouse, rat, or human cerebellum. ATAC-seq was also performed using cerebellar nuclei from the three species.
Publication Title
Species and cell-type properties of classically defined human and rodent neurons and glia.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.
Publication Title
Identification of the cortical neurons that mediate antidepressant responses.
Sample Metadata Fields
Specimen part, Treatment
View Samples