Project description:We describe "SBARRO" a system in which synaptic networks of cells are reconstructed from scRNA-seq data using clonal infectivity paths of barcoded rabies virus RNAs
Project description:Different lesion types were microdissected out from snap-frozen white matter. Brain nuclei were fluorescence-activated nuclear sorted and treated with Transposase Tn5. Gel beads-in-emulsion was generated, barcoded followed by library construction and sequencing.
Project description:Rabies is an ancient infectious disease but still lacking efficient therapeutic approach despite of vaccine. In this study, we have identified a novel cytoplasmic lncRNA, namely rabies virus related lncRNA 1(RVRL1), whose expression in neuronal cells is up-regulated upon the infection of the causative agent of rabies, the neurotropic virus rabies virus (RABV). RVRL1 effectively inhibits RABV infection both in neuronal cells and in a mouse model. RVRL1 binds to EZH2 and disrupts the PRC2 complex, which is consistent with the inverse relationship between RVRL1 expression and the cellular H3K27me3 level. RVRL1 expression positively regulates the expression of PCP4L1 encoding a 10 kD peptide, which is shown to inhibit RABV replication. These findings highlight a novel mechanism for lncRNAs to upregulate the expression of antiviral genes, and define two potential anti-rabies reagents including an antiviral lncRNA and an antiviral peptide.
Project description:Neuroblastoma cells were treated with a barcoded library of >600 genes and one of several standrard of care neuroblastoma compounds (or vehicle control)
Project description:Cortical circuit tracing using modified rabies virus can identify input neurons making direct monosynaptic connections onto neurons of interest. However, challenges remain in our ability to establish the cell type identity of rabies-labeled input neurons. While transcriptomics may offer an avenue to characterize inputs, the extent of rabies-induced transcriptional changes in distinct neuronal cell types remains unclear and whether these changes preclude characterization of rabies-infected neurons according to established transcriptomic cell types is unknown. We used single-nucleus RNA sequencing to survey the gene expression profiles of rabies-infected neurons and assessed their correspondence with established transcriptomic cell types. We demonstrated that when using transcriptome-wide RNA profiles, rabies-infected cortical neurons can be transcriptomically characterized despite global and cell-type-specific rabies-induced transcriptional changes. Notably, we found differential modulation of neuronal marker gene expression, suggesting that caution should be taken when attempting to characterize rabies-infected cells with single genes or small gene sets.
Project description:E14 mouse ES cells were fixed with formaldehyde, and chromatin was collected and sonicated. IP were performed with antobodies for Forkhead box domain containing proteins plus controls. Libraries were generated using MicroPlex Library Preparation Kit from Diagenode. Libraries were cleaned up with AMPure Beads and analysed with Agilent 2100 Bioanalyzer. Libraries are barcoded/
2014-10-15 | E-ERAD-301 | biostudies-arrayexpress
Project description:KiloSEQ of a barcoded library of UBE2I variant ORFs