Single cell RNA sequencing revealing gene expression profile of thalamus from mice at the age of 2 months
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ORGANISM(S): Mus musculus
PROVIDER: GSE269955 | GEO | 2024/08/05
REPOSITORIES: GEO
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Project description:Single cell RNA sequencing revealing gene expression profile of thalamus from mice at the age of 2 months
| PRJNA1124372 | ENA
Project description:Nuclei of the mammalian thalamus are aggregations of neurons with unique architectures and input-output connections, yet the molecular determinants of their organizational specificity remain unknown. By comparing expression profiles of thalamus and cerebral cortex in adult rhesus monkeys we identified transcripts that are unique to dorsal thalamus or to individual nuclei within it. Real-time quantitative polymerase chain reaction and in situ hybridization analyses confirmed the findings. Expression profiling of individual nuclei microdissected from the dorsal thalamus revealed additional subsets of nucleus-specific genes. Functional annotation using Gene Ontology (GO) vocabulary and Ingenuity Pathway analysis revealed over-representation of GO categories related to development, morphogenesis, cell-cell interactions, and extracellular matrix within the thalamus- and nucleus-specific genes-many involved in the Wnt signaling pathway. Examples included the transcription factor TCF7L2, localized exclusively to excitatory neurons, a calmodulin-binding protein PCP4, the bone extracellular matrix molecules SPP1 and SPARC, and other genes involved in axon outgrowth and cell matrix interactions. Other nucleus-specific genes such as CBLN1 are involved in synaptogenesis. The genes identified likely underlie nuclear specification, cell phenotype and connectivity during development and their maintenance in the adult thalamus. Experiment Overall Design: To determine the molecular underpinnings of nuclear specificity in the dorsal thalamus we isolated micro-punches of tissue from nucleus-specific regions and processed them for microarray analysis. Replicate samples from 5 separate dorsal thalamic nuclei were processed and compared to identify genes unique to each region. Affymetrix U133A Gene Chips were used. All of the samples were isolated from untreated adult monkey brain.
2008-06-15 | E-GEOD-6708 | biostudies-arrayexpress
Project description:Previous studies have proved that astrocytes may be a key neural substrate that regulates wakefulness and consciousness recovery from general anesthesia, while the exact molecular target in astrocytes is still unclear. Using virus injection and in vivo fiber photometry in mice, we found both activating astrocytes and knocking down astrocytic Kir4.1 in paraventricular thalamus (PVT) promotes the consciousness recovery from sevoflurane anesthesia. Single-cell RNA sequencing of PVT reveals two distinct cellular subtypes of glutamatergic neurons: PVTGRM and PVTChAT neurons. Patch-clamp recording results proved that Astrocytic Kir4.1-mediated modulation of sevoflurane on PVT mainly works on PVTChAT neurons. Moreover, we found that PVTChAT neurons project mainly to the mPFC. This specific paraventricular thalamus to prefrontal cortex projection is involved in recovery of consciousness from sevoflurane anesthesia indirectly through modulation of astrocytes. In summary, our findings support the novel conception that the volatile anesthetic sevoflurane can inhibit PVT astrocytic Kir 4.1 to maintain and/or increase neuronal firing of PVTChAT neurons, which mainly projects to mPFC and promotes consciousness recovery from anesthesia.
2024-07-20 | GSE240388 | GEO
Project description:Analysis of thalamus and hypothalamus under conditions of visual deprivation by dark-rearing (DR). Animals subjected to DR from birth till postnatal day (P) 14. Results provide insight into the role of visual inputs in the regulation of gene expression in thalamus and hypothalamus during development. RNA sample was taken from thalamus and hypothalamus of 14-day-old mouse reared in standard or dark condition. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.
2014-01-26 | E-GEOD-53136 | biostudies-arrayexpress
Project description:At 3-months after after traumatic brain injury, messenger RNA sequencing was performed on samples from ipsilateral thalamus and perilesional cortex of selected rats with the chronic inflammatory endophenotype, and sham-operated controls.
2022-01-26 | GSE192979 | GEO
Project description:Knowledge of the full repertoire of thalamus cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using single-nuclei RNA sequencing (snRNA-seq), we sequenced the transcriptomes of 32332 single brain cells, revealing a total of four major cell types within the four thalamus sample from mice.
2023-05-10 | GSE227033 | GEO
Project description:At 3-months after after traumatic brain injury, small RNA sequencing was performed on samples from ipsilateral thalamus and perilesional cortex of selected rats with the chronic inflammatory endophenotype, and sham-operated controls.
2022-01-26 | GSE192980 | GEO
Project description:Purpose: We aimed to resolve if there is a matched expression of neuropeptide receptor(s) and their ligand(s) between the sensory trunk of the trigeminal nerve (Pr5) and the ventrobasal hypothalamus on postnatal day 7 (P7) in mice. We hypothesized that a coincidence of neuropeptide expression and release from the ventrobasal thalamus and the cognate receptor(s) for the specific neuropeptide(s) in trigeminal neurons could allow for novel hypotheses be built on intercellular communication between peripheral axons and their postsynaptic targets in the thalamus. Thereby, this work can be informative of the developmental integration of the whisker pathway, one of the major sensory modalities in laboratory rodents. To this end, we used single-cell RNA-seq on cells dissociated from the ventrobasal thalamus and Pr5 on P7. Results: We tested this hypothesis by single-nucleus RNA-seq performed in parallel on the ventrobasal thalamus and Pr5 at P7. At this developmental stage, the ventrobasal thalamus contained two subtypes of Slc17a6+(glutamatergic) neurons, one subtype of Gad1/Gad2+ (GABA) neurons, astroglia, oligodendrocytes, and vascular components (n = 923 nuclei isolated from n = 3 pups of mixed sex). Slc17a6+ neurons, which we recognize as cortically projecting glutamate neurons, co-expressed molecular components underpinning barrel map formation (e.g., Grin1, Adcy1, Prkaca,99 Ache, Slc6a4) and a significant amount of the thalamocortical neuronal marker Cck, while other neuropeptides/hormones were absent or barely present (e.g., Npy, Sst). At the same time, we harvested n = 731 nuclei from the Pr5 by micro-excision at P7, of which ∼98% expressed Slc17a6, thus qualifying, in total or in part, as centrally-projecting sensory neurons. This neuronal cohort harbored axon guidance molecules, and neuropeptide receptors. Conclusions: We suggest that neuropeptides, particularly galanin, could participate in guidance decisions of Pr5 axons given the complementarity of ligand-receptor expression patterns, and that Galr1 expression could be a time locked feature for those neurons that actively undergo neuritogenesis at a given time.
2024-04-01 | GSE230180 | GEO
Project description:The thalamus of the brain acts as a relay station; taking inputs from several parts of the brain and then sending the information to the cortex and vice versa. It is also the structure know to affected in several brain developmental disorders such as schizophrenia, autism spectrum disorders, bipolar disorders etc. Upon in situ hybridisation one can visualise the expression of the transcription factor Tcf7l2 to be highest in prosomeric regions of the thalamus throughout development. With this information in mind we set out to find out, if the expression of Tcf7l2 is essential for the identity of the thalamic structure. Therefore, Tcf7l2 was knocked (KO) out using Cre+mice at embryonic stage E18.5 and postnatal adult stage P60. The E18.5 Tcf7l2 KO is a total knockout and the P60 Tcf7l2 KO is neuron-specific knockout. Total RNA was extracted and sent for sequencing using Illumina 2500. The data obtained was aligned by HISAT2 alignment tool, and the excon read counts were gathered using htseq counts, and expression normalization and differential gene expression was analysed using DESeq2.
2020-02-10 | E-MTAB-8755 | biostudies-arrayexpress
Project description:Analysis of thalamus and hypothalamus under conditions of visual deprivation by dark-rearing (DR). Animals subjected to DR from birth till postnatal day (P) 14. Results provide insight into the role of visual inputs in the regulation of gene expression in thalamus and hypothalamus during development.
2014-01-26 | GSE53136 | GEO