Published in STAR Protocols
Spatially resolved transcriptomics (SrT) allows us to explore organ/tissue architecture from the angle of the gene programs involved in their molecular complexity. Here, we describe the use of MULTILAYER to reveal molecular tissue substructures from the analysis of localized transcriptomes (defined as gexels). MULTILAYER can process low- and high-r...
Published in STAR Protocols
Published in STAR Protocols
Multiple downstream analyses are necessary to interpret the output of bacterial pangenome reconstruction software. This requires integrating diverse kinds of genetic and phenotypic data, which to date are left to each user’s criterion. To fill this gap, we created Pagoo, a pangenome post-processing tool that leverages a standardized but flexible an...
Published in STAR Protocols
This protocol describes the assembly and use of MitoPunch to deliver mitochondria containing mitochondrial DNA (mtDNA) into cells lacking mtDNA (ρ0 cells). MitoPunch generates stable isolated mitochondrial recipient clones with restored mtDNA and recovered respiration, enabling investigation of mtDNA mutations and mtDNA-nuclear DNA interactions in ...
Published in STAR Protocols
Hematopoietic stem and progenitor cells (HSPCs) reside in the bone marrow and supply blood cells. Efficient methods for isolation of HSPCs are required. Here, we present protocols for the isolation of human and murine HSPCs using manual and FACS-assisted techniques. Isolated HSPCs can be used for downstream applications, including colony forming un...
Published in STAR Protocols
Many cancers, including leukemias, are dynamic oligoclonal diseases. Tools to identify and prospectively isolate genetically distinct clones for functional studies are needed. We describe our CombiFlow protocol, which is a combinatorial flow cytometry-based approach to identify and isolate such distinct clones. CombiFlow enables the visualization o...
Published in STAR Protocols
About 150 modifications have been identified in RNA species. Besides their regulatory roles in the intracellular gene expression, abundant modified RNA nucleosides are catabolized from RNA and released into extracellular fluids, which can impact extracellular signaling as ligands for receptors. Here, we describe a protocol to prepare samples from b...
Published in STAR Protocols
Oxidized phosphatidylcholine (OxPC) found in multiple sclerosis brain lesions mediates neurodegeneration. Microglia are prominent responders to the OxPC insult, and thus, studying their protective or noxious functions is important to help halt neurodegeneration. Here, we present protocols including cell isolation and culture, animal surgeries, as w...
Published in STAR Protocols
Published in STAR Protocols
Because glioblastoma (GBM) exhibits high heterogeneity, it is desirable to use patient-derived cells from the first stage of screening for GBM drug discovery. Here, we describe a protocol to culture patient-derived GBM cells on the extracellular matrix-coated plates to allow high-throughput screening. Further, we detail approaches to identify the m...
