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Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

ABSTRACT: Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

PROVIDER: PRJNA481681 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7535550_1.fastq.gz	Fastqsanger.gz
	SRR7535550_2.fastq.gz	Fastqsanger.gz
	SRR7535551_1.fastq.gz	Fastqsanger.gz
	SRR7535551_2.fastq.gz	Fastqsanger.gz
	SRR7535552_1.fastq.gz	Fastqsanger.gz

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Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

Project description:Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

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Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

Project description:Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

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Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

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Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

Project description:We apply geographical position sequencing (Geo-seq), a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology, to investigate the heterogeneous nature of suprachiasmatic nucleus (SCN) in adult mouse. The 3D quantitative data enables spatial gene expression pattern visualization . The dataset identified genes that are coexpressed in a specific region, mark domains of similar global pattern of expression, and can be used for mapping the position of single cells dissociated from adult SCN.

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Transcriptome profiling of the mouse suprachiasmatic nucleus at single cell resolution

Project description:Transcriptome profiling of the mouse suprachiasmatic nucleus at single cell resolution

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Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

Project description:Mammalian circadian behaviors are orchestrated by suprachiasmatic nucleus (SCN) in the hypothalamus. Yet basic SCN cell types and their roles in circadian pacemaking are still unclear. In this study, we comprehensively characterized the basic cell types of SCN and their circadian and light-induced gene expression. In SCN, we identified seven major cell types among which neurons, astrocytes, ependymocytes and endothelial cells display cell-type specific circadian gene expression. We found that five SCN neuron subtypes, Avp+/Nms+, Vip+/Nms+, Vip+/Grp+, Cck+/C1ql3+ and Cck+/Bdnf+, differ in their spatial distribution, circadian rhythmicity and light responsiveness. Among the rhythmic neuron subtypes, we observed a wave of circadian gene expression propagating from the subtypes in posterior SCN to the subtypes in anterior SCN. Such wave can be explained by the neuropeptide-receptor signaling network in which Avp+/Nms+ subtype is the leader of circadian oscillations. Our study provides insights into the basic neural mechanism of circadian pacemaking in mammals.

2019-06-19 | GSE132608 | GEO

Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

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Transcriptome expressed in the mouse suprachiasmatic nucleus

2011-04-22 | GSE28574 | GEO

Transcriptome expressed in the mouse suprachiasmatic nucleus

Project description:This array set was used to identify the genes that are highly expressed in the mouse suprachiasmatic nucleus (SCN). Because pharmacological inhibition of Gai/o activity with pertussis toxin hampers intercellular synchronization and causes dampened rhythms of the entire SCN, we hypothesized that member(s) of the Regulator of G protein Signaling (RGS) family might contribute to synchronized cellular oscillations in the SCN. To test this hypothesis, we surveyed all known mouse Rgs genes for their expression by using GeneChip and selected the genes that are highly expressed in the SCN for further analysis. 12h light:12h dark cycle entrained animals were released into constant darkess. SCN punches were taken from 10 animals at CT2 and 10 animals at CT14, pooled together, and subjected to DNA microarray analysis. CT2 and CT14 correspond, respectively, to 2 and 14 hours after presumptive onset of daytime under constant darkness.

2011-04-22 | E-GEOD-28574 | biostudies-arrayexpress

Transcriptome profiling of the mouse suprachiasmatic nucleus at single cell resolution

Project description:Circadian rhythms are governed by the hypothalamic suprachiasmatic nucleus (SCN) which consists of ca. 20,000 cellular oscillators bound together in a powerful time-keeping network. The goal of this study was to characterise its component cells and network structure by conducting single-cell sequencing of SCN organotypic slices. scRNASeq libraries were prepared using 10x Genomics Chromium Single Cell 3’ Library and Gel Bead v2 kit. SCN cells, diluted in 0.04% BSA-nuclease-free water, reverse transcription master mix and partitioning oil, were loaded on a ChromiumTM Single Cell A Chip and run on the Chromium Controller to obtain at target cell recovery rate of 8,000 cells. Final libraries were sequenced on one flow cell of an Illumina HiSeq 4000 with a read length of 26bp for read 1 (cell barcode and unique molecule identifier and sample barcode) and 98bp for read 2 (RNA read) to yield approximately 340 million reads per sample. We sequenced 13,324 cells from 52 SCN slices at circadian time 7.5 (mid-day) over three independent sequencing runs, and 16,996 cells from 36 SCN slices at circadian time 15.5 (mid-night) over two independent sequencing runs.

2021-09-06 | GSE167927 | GEO

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