Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Adult mouse SVZ niche at the single cell resolution

ABSTRACT: Single cell RNA-seq of SVZ lateral ventricle walls from non-irradiated mice brains and 5 days post-irradiation 4Gy-irradiated mice brains (according to the model SVZ regeneration after a moderate dose of irradiation that we previously described (Daynac et al. 2013). We used this model of SVZ reconstitution to gain insights on the annotation and and temporal ordering of neural progenitors clusters.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Chicheportiche Alexandra

PROVIDER: E-MTAB-12495 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Quiescent neural stem cells exit dormancy upon alteration of GABAAR signaling following radiation damage.

Daynac Mathieu M Chicheportiche Alexandra A Pineda Jose R JR Gauthier Laurent R LR Boussin François D FD Mouthon Marc-André MA

Stem cell research 20130308 1

Quiescent neural stem cells (NSCs) are considered the reservoir for adult neurogenesis, generating new neurons throughout life. Until now, their isolation has not been reported, which has hampered studies of their regulatory mechanisms. We sorted by FACS quiescent NSCs and their progeny from the subventricular zone (SVZ) of adult mice according to the expression of the NSC marker LeX/CD15, the EGF receptor (EGFR) and the CD24 in combination with the vital DNA marker Hoechst 33342. Characterizati ...[more]

PMID: 23562833

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Project description:Histone 3 lysine 4 trimethylation (H3K4me3) is known to be associated with transcriptionally active or poised genes and required for postnatal neurogenesis within the subventricular zone (SVZ) in the rodent model. Previous comparisons have shown significant correlation between baboon (Papio anubis) and human brain. In this study, we demonstrate that chromatin activation mark H3K4me3 is present in undifferentiated progenitor cells within the SVZ of adult baboon brain. To identify the targets and regulatory role of H3K4me3 within the baboon SVZ, we developed a technique to purify undifferentiated SVZ cells while preserving the endogenous nature without introducing culture artifact to maintain the in vivo chromatin state for genome-wide studies (ChIP-Seq and RNA-Seq). We identified that H3K4me3 is significantly enriched for genes involved in cell cycle, cell signaling, nervous system development, metabolism, and ribosomal biogenesis. Among these genes, RNA-Seq identified that genes associated with cellular signaling/maintenance, DNA replication, metabolism, and protein synthesis are expressed. We found that 72% of H3K4me3-enriched genes in undifferentiated SVZ cells are expressed (1913 genes are detectable by RNA-Seq; 2663 genes enriched with H3K4me3 by ChIP-Seq). On the other hand, 750 out of total 2663 H3K4me3-enriched genes are not detectable by RNA-Seq, suggesting 28% of genes in SVZ are poised for activation. RNA-seq profiles were generated from adult baboon subventricular zone primary cells by paired-end deep sequencing with an Illumina HiSeq 2000. RNA-Seq Analysis: Total RNA was extracted from purified baboon SVZ cells using TRIzol reagent, and sequencing libraries were generated with the Illumina RNA-Seq library kit. Paired-end RNA-deepSeq (76 base pair; >300 million tag reads; 269,081,636 mapped reads) were aligned to hg19. DESeq was used to normalize raw read counts, and Cufflink reports read counts and estimated FPKM (fragments per kilobase of exon per million fragments mapped; http://cufflinks.cbcb.umd.edu/faq.html#fpkm). Genes with expression values >1 FPKM were considered for subsequent analyses.

Dataset Information

Adult mouse SVZ niche at the single cell resolution

Publications

Quiescent neural stem cells exit dormancy upon alteration of GABAAR signaling following radiation damage.

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