Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of eye opening on gene expression in the superficial layers of the rat superior colliculus

ABSTRACT: We performed RNA-seq on six samples of P20 Sprague Dawley rat superior colliculus, three control rats that underwent eye opening at P14 until P20 and three deprived rats which had their eyes glued closed from P14 until P20. Each sample was created from two pooled colliculi.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE72787 | GEO | 2015/09/09

SECONDARY ACCESSION(S): PRJNA295072

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effects of eye opening on gene expression in the superficial layers of the rat superior colliculus

Project description:We performed RNA-seq on six samples of P20 Sprague Dawley rat superior colliculus, three control rats that underwent eye opening at P14 until P20 and three deprived rats which had their eyes glued closed from P14 until P20. Each sample was created from two pooled colliculi. RNA-seq of the superior colliculus with and without long term light deprivation.

2015-09-09 | E-GEOD-72787 | biostudies-arrayexpress

GABAergic cell types in the superficial layers of the mouse superior colliculus.

Project description:To begin to unravel the complexities of GABAergic circuits in the superior colliculus (SC), we utilized mouse lines that express green fluorescent protein (GFP) in cells that contain the 67 kDa isoform of glutamic acid decarboxylase (GAD67-GFP), or Cre-recombinase in cells that contain glutamic acid decarboxylase (GAD; GAD2-cre). We used Cre-dependent virus injections in GAD2-Cre mice and tracer injections in GAD67-GFP mice, as well as immunocytochemical staining for gamma amino butyric acid (GABA) and parvalbumin (PV) to characterize GABAergic cells that project to the pretectum (PT), ventral lateral geniculate nucleus (vLGN) or parabigeminal nucleus (PBG), and interneurons in the stratum griseum superficiale (SGS) that do not project outside the SC. We found that approximately 30% of SGS neurons in the mouse are GABAergic. Of these GABAergic neurons, we identified three categories of potential interneurons in the GAD67-GFP line (GABA+GFP ~45%, GABA+GFP + PV ~15%, and GABA+PV ~10%). GABAergic cells that did not contain GFP or PV were identified as potential projection neurons (GABA only ~30%). We found that GABAergic neurons that project to the PBG are primarily located in the SGS and exhibit narrow field vertical, stellate, and horizontal dendritic morphologies, while GABAergic neurons that project to the PT and vLGN are primarily located in layers ventral to the SGS. In addition, we examined GABA and GAD67-containing elements of the mouse SGS using electron microscopy to further delineate the relationship between GABAergic circuits and retinotectal input. Approximately 30% of retinotectal synaptic targets are the presynaptic dendrites of GABAergic interneurons, and GAD67-GFP interneurons are a source of these presynaptic dendrites.

| S-EPMC6888991 | biostudies-literature

Modular organization of the motor space in the mouse superior colliculus

Project description:In order to characterize the genetic diversity within the Stratum Griseum Intermediale (SGI), we screened gene expression by extracting RNA from sensory and motor layers of the Superior Colliculus (SC) at post-natal day (P)7.

2019-07-31 | GSE135082 | GEO

Mapping Visual Functions onto Molecular Cell Types in the Mouse Superior Colliculus

Project description:To facilitate investigation of function, connectivity, and development of superficial superior colliculus (sSC), we identified 28 neuron subtypes and subtype-enriched marker genes from tens of thousands of adult mouse sSC neurons

2023-04-21 | GSE223155 | GEO

Spatial updating in monkey superior colliculus in the absence of the forebrain commissures: dissociation between superficial and intermediate layers.

Project description:In previous studies, we demonstrated that the forebrain commissures are the primary pathway for remapping from one hemifield to the other. Nonetheless, remapping in lateral intraparietal cortex (LIP) across hemifield is still present in split brain monkeys. This finding indicates that a subcortical structure must contribute to remapping. The primary goal of the current study was to characterize remapping activity in the superior colliculus in intact and split brain monkeys. We recorded neurons in both the superficial and intermediate layers of the SC. We found that across-hemifield remapping was reduced in magnitude and delayed compared with within-hemifield remapping in the intermediate layers of the SC in split brain monkeys. These results mirror our previous findings in area LIP. In contrast, we found no difference in the magnitude or latency for within- compared with across-hemifield remapping in the superficial layers. At the behavioral level, we compared the performance of the monkeys on two conditions of a double-step task. When the second target remained within a single hemifield, performance remained accurate. When the second target had to be updated across hemifields, the split brain monkeys' performance was impaired. Remapping activity in the intermediate layers was correlated with the accuracy and latency of the second saccade during the across-hemifield trials. Remapping in the superficial layers was correlated with latency of the second saccade during the within- and across-hemifield trials. The differences between the layers suggest that different circuits underlie remapping in the superficial and intermediate layers of the superior colliculus.

| S-EPMC2944681 | biostudies-literature

Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus

Project description:Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus

| PRJNA1026945 | ENA

Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus – Pten

Project description:The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. The developmental principles directing the generation of SC cell-type diversity are however not understood. Here we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic MADM (Mosaic Analysis with Double Markers)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally-related cell lineages revealed that radial glial progenitor (RGP) cells in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at single RGP/cell level of the mammalian SC ontogeny

2023-11-03 | GSE245104 | GEO

Molecular features distinguish ten neuronal types in the mouse superficial superior colliculus.

Project description:The superior colliculus (SC) is a midbrain center involved in controlling head and eye movements in response to inputs from multiple sensory modalities. Visual inputs arise from both the retina and visual cortex and converge onto the superficial layer of the SC (sSC). Neurons in the sSC send information to deeper layers of the SC and to thalamic nuclei that modulate visually guided behaviors. Presently, our understanding of sSC neurons is impeded by a lack of molecular markers that define specific cell types. To better understand the identity and organization of sSC neurons, we took a systematic approach to investigate gene expression within four molecular families: transcription factors, cell adhesion molecules, neuropeptides, and calcium binding proteins. Our analysis revealed 12 molecules with distinct expression patterns in mouse sSC: cadherin 7, contactin 3, netrin G2, cadherin 6, protocadherin 20, retinoid-related orphan receptor β, brain-specific homeobox/POU domain protein 3b, Ets variant gene 1, substance P, somatostatin, vasoactive intestinal polypeptide, and parvalbumin. Double labeling experiments, by either in situ hybridization or immunostaining, demonstrated that the 12 molecular markers collectively define 10 different sSC neuronal types. The characteristic positions of these cell types divide the sSC into four distinct layers. The 12 markers identified here will serve as valuable tools to examine molecular mechanisms that regulate development of sSC neuronal types. These markers could also be used to examine the connections between specific cell types that form retinocollicular, corticocollicular, or colliculothalamic pathways. J. Comp. Neurol. 524:2300-2321, 2016. © 2016 Wiley Periodicals, Inc.

| S-EPMC4892959 | biostudies-literature

Chronic chemogenetic activation of the superior colliculus in glaucomatous mice: local and retrograde molecular signature

Project description:One important facet of the glaucoma pathology is axonal damage, which ultimately disrupts the connection between the retina and its postsynaptic targets. The concurrent loss of retrograde support interferes with the functionality and survival of the retinal ganglion cells (RGCs). Con-versely, previous research has shown that stimulation of neuronal activity in a primary retinal target area—i.e., the superior colliculus— promotes RGC survival in an acute mouse model of glaucoma. To build further on this observation, we applied repeated chemogenetics in the superior colliculus of a more chronic model of glaucoma—i.e., the microbead occlusion model—and per-formed bulk RNA sequencing on collicular lysates and isolated RGCs. Our study revealed that chronic target stimulation upon glaucomatous injury phenocopies the a priori expected molecular response: growth factors were pinpointed as essential transcriptional regulators both in the locally stimulated tissue and in distant, unstimulated RGCs. Strikingly, and although the RGC tran-scriptome revealed an enrichment of pro-survival signaling pathways, functional rescue of injured RGCs was not achieved.

2022-06-15 | GSE202012 | GEO

Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus – Pten

Project description:Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus – Pten

| PRJNA1026955 | ENA