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Deep single-cell RNAseq of Gpnmb+Clec7a+ microglia from postnatal day 7 cerebellum

ABSTRACT: Deep single-cell RNAseq of Gpnmb+Clec7a+ microglia from postnatal day 7 cerebellum

PROVIDER: PRJNA507268 | ENA |

REPOSITORIES: ENA

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Deep single-cell RNAseq of Gpnmb+Clec7a+ microglia from postnatal day 7 cerebellum

Project description:We generated single-cell RNAseq profiles of 143 microglia, sorted in the gate CD45lowCD11+Gpnmb+Clec7a+, from postnatal day 7 cerebellum to validate the newly identified “proliferative region-associated microglia (PAM)” (Gpnmb and Clec7a are PAM surface markers). Single cells were FACS index sorted followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). These cells showed characteristic PAM gene expression and clustered together with other PAM cells sequenced in the same study.

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Project description:We generated single-cell RNAseq profiles of 369 microglia (183 from wild type and 186 from Trem2 knock-out), sorted in the gate CD45lowCD11+ or CD45lowCD11+Gpnmb+Clec7a+ (PAM enrichment), to compare gene expression of wild type vs. Trem2 knock-out microglia on the postnatal day 7. Single cells were FACS index sorted from the whole brain followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). A total of 334 cells passed quality control for data analysis. Microglia in the Trem2 knock-out contained a similar PAM population with characteristic gene expression, suggesting that the presence of early postnatal PAM do not depend on TREM2.

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Unique microglia expression profile in developing white matter.

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Postnatal day 6 cerebellum of Ts65Dn and TcMAC21 Down syndrome mouse models

Project description:Postnatal day 6 cerebellum of Ts65Dn and TcMAC21 Down syndrome mouse models

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Single-Cell Transcriptomes Reveal Molecular Specializations of Neuronal Cell Types in the Developing Cerebellum

Project description:We analyzed transcriptome profiles of 21,119 single cells of the postnatal mouse cerebellum and identified 8 main cell clusters (Granule precursors, Granule cells, Astrocytes, Interneurons, Oligodendrocytes, Microglia, Purkinje cells, Endothelial cells).

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Postnatal day 6 cerebellum of Ts65Dn and TcMAC21 Down syndrome mouse models

Project description:Dysregulation of Sonic hedgehog (SHH) signaling may contribute to multiple Down syndrome-associated phenotypes, including cerebellar hypoplasia, congenital heart defects, craniofacial and skeletal dysmorphologies, and Hirschsprung disease. Granule cell precursors isolated from the developing cerebellum of Ts65Dn mice are less responsive to the mitogenic effects of SHH than euploid cells, and a single postnatal dose of the SHH pathway agonist SAG rescues cerebellar morphology and performance on learning and memory tasks in Ts65Dn mice. SAG treatment also normalizes expression levels of OLIG2 in neural progenitor cells derived from human trisomy 21 iPSCs. However, despite evidence that activating SHH signaling rescues Down syndrome-associated phenotypes, chromosome 21 does not encode any canonical components of the SHH pathway. Here, we screened 163 chromosome 21 cDNAs in a series of SHH-responsive cell lines to identify chromosome 21 genes that modulate SHH signaling and confirmed overexpression of trisomic candidate genes using RNA-seq in Ts65Dn and TcMAC21 cerebellum. Our study indicates that some chromosome 21 genes, including DYRK1A, activate SHH signaling while others, such as HMGN1 and MIS18A, inhibit SHH signaling. Moreover, overexpression of genes involved in chromatin structure and mitosis, but not genes previously implicated in ciliogenesis, regulate the SHH pathway. Our data suggest that cerebellar hypoplasia and other phenotypes related to aberrant SHH signaling arise from the net effect of trisomy for multiple chromosome 21 genes rather than the overexpression of a single trisomic gene. Identifying which chromosome 21 genes modulate SHH signaling may also suggest new therapeutic avenues for ameliorating Down syndrome phenotypes.

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Analysis Of Molecular Networks In The Cerebellum In Chronic Schizophrenia: Modulation By Early Postnatal Life Stressors In Murine Models

Project description:Despite the growing importance of the cortico-cerebellar-thalamo-cortical circuit in schizophrenia, limited information is available regarding altered molecular networks in cerebellum. To identify altered protein networks, we conducted proteomic analysis of grey matter of postmortem cerebellar cortex in chronic schizophrenia subjects (n=12) and healthy individuals (n=14) followed by an extensive bioinformatic analysis. Two double-hit postnatal stress murine models for SZ were used to validate the most robust candidates.

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