Project description:The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed 10 differentiated distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous novel marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSN) which have specific markers and which overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states. We measured the transcriptome of 1208 single striatal cells using two complementary approaches; microfluidic single-cell RNAseq (Mic-scRNAseq) and single cell isolation by FACS (FACS-scRNAseq) (Table S1). We sampled cells either randomly or enriched specifically for MSNs or astrocytes using FACS from D1- tdTomato (tdTom)/D2-GFP or Aldhl1-GFP mice, respectively
Project description:PURPOSE: To provide a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. One third of the unique tags were expressed at both stages, whereas a third was identified exclusively in PN9 or adult corneas. Three hundred thirty-four PN9 and 339 adult tags were enriched more than fivefold over other published nonocular libraries. Abundant transcripts were associated with metabolic functions, redox activities, and barrier integrity. Three members of the Ly-6/uPAR family whose functions are unknown in the cornea constitute more than 1% of the total mRNA. Aquaporin 5, epithelial membrane protein and glutathione-S-transferase (GST) omega-1, and GST alpha-4 mRNAs were preferentially expressed in distinct corneal epithelial layers, providing new markers for stratification. More than 200 tags were differentially expressed, of which 25 mediate transcription. CONCLUSIONS: In addition to providing a detailed profile of expressed genes in the PN9 and mature mouse cornea, the present SAGE data demonstrate dynamic changes in gene expression after eye opening and provide new probes for exploring corneal epithelial cell stratification, development, and function and for exploring the intricate relationship between programmed and environmentally induced gene expression in the cornea. Keywords: other
Project description:Selvarasu2009 - Genome-scale metabolic
network of Mus Musculus (iSS724)
This model is described in the article:
Genome-scale modeling and in
silico analysis of mouse cell metabolic network.
Selvarasu S, Karimi IA, Ghim GH, Lee
DY.
Mol Biosyst 2010 Jan; 6(1):
152-161
Abstract:
Genome-scale metabolic modeling has been successfully
applied to a multitude of microbial systems, thus improving our
understanding of their cellular metabolisms. Nevertheless, only
a handful of works have been done for describing mammalian
cells, particularly mouse, which is one of the important model
organisms, providing various opportunities for both biomedical
research and biotechnological applications. Presented herein is
a genome-scale mouse metabolic model that was systematically
reconstructed by improving and expanding the previous generic
model based on integrated biochemical and genomic data of Mus
musculus. The key features of the updated model include
additional information on gene-protein-reaction association,
and improved network connectivity through lipid, amino acid,
carbohydrate and nucleotide biosynthetic pathways. After
examining the model predictability both quantitatively and
qualitatively using constraints-based flux analysis, the
structural and functional characteristics of the mouse
metabolism were investigated by evaluating network
statistics/centrality, gene/metabolite essentiality and their
correlation. The results revealed that overall mouse metabolic
network is topologically dominated by highly connected and
bridging metabolites, and functionally by lipid metabolism that
most of essential genes and metabolites are from. The current
in silico mouse model can be exploited for understanding and
characterizing the cellular physiology, identifying potential
cell engineering targets for the enhanced production of
recombinant proteins and developing diseased state models for
drug targeting.
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