Published in STAR protocols
The mammalian brain has over 10,000 types of neurons. Therefore, studying gene regulation in the brain requires effective strategies for targeting specific cell types, especially those in low abundance. Cell isolation may alter gene expression and is disruptive to mature neurons with extensive processes. This protocol describes cell-type-specific e...
Published in STAR protocols
We developed an adeno-associated virus (AAV) vector-based technique to label mouse neostriatal neurons comprising direct and indirect pathways with different fluorescent proteins and analyze their axonal projections. The AAV vector expresses GFP or RFP in the presence or absence of Cre recombinase and should be useful for labeling two cell populati...
Published in STAR protocols
The Fused (Fu) kinase is a key transducer of Hedgehog signaling, but its relevant substrates have remained obscured due to the difficulty of obtaining active Fu for in vitro kinase assay. Based on the mechanism of Fu activation in vivo, we engineered a constitutively active Fu and expressed it in Sf9 cells using the baculovirus system. The kinase w...
Published in STAR protocols
IFI16 is an important player of the host intrinsic immune response. Among others, it has been reported to sense intermediate products of HIV-1 reverse transcription in the cytosol and to sequester the transcription factor Sp1 in the nucleus to attenuate viral gene expression. Here, we present three different methods to reduce IFI16 protein expressi...
Published in STAR protocols
Lectin histochemical analysis of tissues combined with immunohistochemistry is a valuable tool to characterize and correlate the spatial distribution of glycans with the presence of specific cell types or antigens of interest. The current protocol describes the application of monosaccharide motif specificity of lectin binding to glycan residues to ...
Published in STAR protocols
Immune cells, such as macrophages, reprogram their lipid metabolism in response to the activation of pattern recognition receptors (e.g., TLRs, NLRs) and cytokine receptors (e.g., interferons, interleukins). Profiling these changes can be achieved with shotgun mass spectrometry. This protocol provides step-by-step instructions on the generation and...
Published in STAR protocols
Translation regulation is a fundamental step in gene regulation with critical roles in neurodevelopment. Here, we describe three protocols to calculate the ribosomal-engagement levels of the transcriptome from in vitro-derived neuronal cells. The protocols described here include enrichment of in vitro-generated pluripotent-derived neurons, immunoaf...
Published in STAR protocols
Adult neurogenesis, a process of generating newborn neurons from adult neural stem cells, is required for brain homeostasis, cognition, and affective behaviors. Deciphering the molecular mechanisms underlying adult neurogenesis will provide valuable insights into the functional integrity of the adult brain and the etiology of neurological disorders...
Published in STAR protocols
The recruitment of the minichromosome maintenance complex (MCM) on DNA replication origins is a critical process for faithful genome duplication termed licensing. Aberrant licensing has been associated with cancer and, recently, with neurodevelopmental diseases. Investigating MCM loading in complicated tissues, such as brain, remains challenging. H...
Published in STAR protocols
RNA-binding proteins are key regulators of cell identity and function, which underscores the need for unbiased and versatile protocols to identify and characterize novel protein-RNA interactions. Here, we describe a simple and cost-effective in vitro RNA immunoprecipitation (iv-RIP) method to assess the direct or indirect RNA-binding ability of any...
