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Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[bulk RNA-seq]

ABSTRACT: Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[bulk RNA-seq]

PROVIDER: PRJNA1074759 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27923011_1.fastq.gz	Fastqsanger.gz
	SRR27923011_2.fastq.gz	Fastqsanger.gz
	SRR27923012_1.fastq.gz	Fastqsanger.gz
	SRR27923012_2.fastq.gz	Fastqsanger.gz
	SRR27923013_1.fastq.gz	Fastqsanger.gz

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Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[bulk RNA-seq]

Project description:We generated a comprehensive dataset utilizing the cuprizone model. This dataset encompasses bulk RNA-seq, single-nucleus RNA-seq (snRNA-seq), and spatial transcriptomics, with the aim of investigating the molecular changes linked to the cuprizone-induced demyelination phenotype. Integration of these omics dataset allowed us to investigate the changes occurring at both the single-cell and spatial levels, thereby enabling a deeper understanding of the cellular dynamics and molecular interactions associated with the cuprizone-induced demyelination phenotype.

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Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[Spatial Transcriptomics]

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Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[Spatial Transcriptomics]

Project description:Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[Spatial Transcriptomics]

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Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level

Project description:Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level

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Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[snRNA-seq]

Project description:Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[snRNA-seq]

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Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level

Project description:This SuperSeries is composed of the SubSeries listed below.

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Bulk RNAseq of AnnexinV+ and AnnexinV- cells from the Mertk-KO corpus callosum at the 4 week cuprizone timepoint

Project description:Purpose: Following 4 weeks of 0.2% cuprizone treatment, Mertk-KO mice accumulate dying cells in the corpus callosum (based on cleaved-cas3 staining). These cells are not seen in Mertk-WT animals at the same cuprizone timepoint. The goal of this study is to identify these dying cells in the Mertk-KO corpus callosum Methods: 2 biological replicates (mice) were used. Corpus callosa were dissected from Mertk-KO mice after 4 weeks of 0.2% cuprizone treatment. Tissues were dissected into single cells using Miltenyi Neural Tissue Dissociation Kit (P) and stained with Annexin V. The stained cell suspensions were then FAC sorted into Annexin V+ and Annexin V- populations. RNA from these cells were extracted using QIAGEN RNeasy kit. Results: Bulk RNA-Seq data were analyzed using an in-house pipeline consisting of GSNAP HTSeqGenie. Reads aligning uniquely to exons were counted to each gene, and size-factor normalization was used to calculating nRPKM statistic. Conclusions: Based on the differences of transcriptomic profiles of AnnexinV+ and AnnexinV- cells, we conclude that the dying AnnexinV+ cells are microglia.

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Project description:Corpus callosum bulk RNA sequencing of a cuprizone mouse model of demyelination

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