Filters
Technology
Platform
GSE31434
Homo sapiens
12 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We identified SLC44A5 as a gene associated with birth weight in cattle based on genome wide association studies.
Publication Title
The molecular effects of a polymorphism in the 5'UTR of solute carrier family 44, member 5 that is associated with birth weight in Holsteins.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Evidence that bovine forebrain embryonic zinc finger-like gene influences immune response associated with mastitis resistance.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To investigate genes that might influence resistance to infection through IGF1R, we screened human breast cancer-derived OCUB-M cells transfected with expression vector encoding IGF1R using microarray analysis.
Publication Title
Evidence that bovine forebrain embryonic zinc finger-like gene influences immune response associated with mastitis resistance.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To identify genes that influence resistance to mastitis, we scanned
Publication Title
Evidence that bovine forebrain embryonic zinc finger-like gene influences immune response associated with mastitis resistance.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
Illumina HiSeq 2500
Description
Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome atlas of gene expression for every excitatory neuronal class in the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical neurons of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell class- and region-specific transcriptional atlas for these canonical populations. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population
Publication Title
Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 21 Downloadable Samples
- Illumina HiSeq 2500
Description
AGRP neurons are a hypothalamic population that senses physiological energy deficit and consequently increases appetite. Molecular and cellular processes for energy-sensing and elevated neuronal output are critical for understanding the central nervous system response to energy deficit states, such as during weight-loss. Cell type-specific transcriptomics can be used to identify pathways that counteract weight-loss but, in adult mice, this has been limited by technical challenges. We report high-quality gene expression profiles of AGRP neurons under well-fed and energy deficit states. For comparison, we also analyzed POMC neurons, an intermingled population that suppresses appetite. This data newly identifies cell type-selective involvement of signaling pathways, ion channels, neuropeptides, and G-protein coupled receptors. Combined with methods to validate and manipulate these pathways, this resource greatly expands molecular insight into neuronal regulation of body weight, and may be useful for devising therapeutic strategies for obesity and eating disorders. Overall design: Examination of 2 different neuronal cell types under 2 conditions.
Publication Title
Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Fast-spiking (FS) interneurons are important elements of neocortical circuitry that constitute the primary source of synaptic inhibition in adult cortex and impart temporal organization on ongoing cortical activity. The highly specialized intrinsic membrane and firing properties that allow cortical FS interneurons to perform these functions are attributable to equally specialized gene expression, which is ultimately coordinated by cell-type-specific transcriptional regulation. Although embryonic transcriptional events govern the initial steps of cell-type specification in most cortical interneurons, including FS cells, the electrophysiological properties that distinguish adult cortical cell types emerge relatively late in postnatal development, and the transcriptional events that drive this maturational process are not known. To address this, we used mouse whole-genome microarrays and whole-cell patch clamp to characterize the transcriptional and electrophysiological maturation of cortical FS interneurons between postnatal day 7 (P7) and P40. We found that the intrinsic and synaptic physiology of FS cells undergoes profound regulation over the first 4 postnatal weeks and that these changes are correlated with primarily monotonic but bidirectional transcriptional regulation of thousands of genes belonging to multiple functional classes. Using our microarray screen as a guide, we discovered that upregulation of two-pore K leak channels between P10 and P25 contributes to one of the major differences between the intrinsic membrane properties of immature and adult FS cells and found a number of other candidate genes that likely confer cell-type specificity on mature FS cells.
Publication Title
Transcriptional and electrophysiological maturation of neocortical fast-spiking GABAergic interneurons.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 47 Downloadable Samples
- Illumina HiSeq 2500
Description
Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability. Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Overall design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population
Publication Title
Spatial Gene-Expression Gradients Underlie Prominent Heterogeneity of CA1 Pyramidal Neurons.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 42 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
The mammalian forebrain is a tissue of stunning complexity comprised of numerous regions each containing many distinct cell types that differ in their intrinsic and synaptic physiology, morphology and connectivity. These differences are likely conferred by differential gene expression, but the extent and nature of cell type specific gene expression is largely unknown. Here, we carried out microarray analysis of twelve major classes of fluorescently labelled neurons within the forebrain and provide the first comprehensive view of gene expression differences. The results demonstrate a profound molecular heterogeneity among neuronal subtypes, represented disproportionately by gene paralogs, and begin to reveal the genetic programs underlying the fundamental divisions between neuronal classes including that between glutamatergic and GABAergic neurons.
Publication Title
Molecular taxonomy of major neuronal classes in the adult mouse forebrain.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 32 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Mutations in methyl-CpG-binding protein 2 (MeCP2) cause Rett syndrome and related autism spectrum disorders. MeCP2 is believed to be required for proper regulation of brain gene expression, but prior microarray studies in Mecp2 knockout mice using brain tissue homogenates have revealed only subtle changes in gene expression. Here, by profiling discrete subtypes of neurons we uncovered more dramatic effects of MeCP2 on gene expression, overcoming the "dilution problem" associated with assaying homogenates of complex tissues. The results reveal misregulation of genes involved in neuronal connectivity and communication. Importantly, genes up-regulated following loss of MeCP2 are biased toward longer genes but this is not true for down-regulated genes, suggesting MeCP2 may selectively repress long genes. Since genes involved in neuronal connectivity and communication, such as cell adhesion and cell-cell signaling genes, are enriched among longer genes, their misregulation following loss of MeCP2 suggests a possible etiology for altered circuit function in Rett syndrome.
Publication Title
Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples