2024
Image-based 3D genomics through chromatin tracing
Yang T, Wang S. Image-based 3D genomics through chromatin tracing. Nature Reviews Methods Primers 2024, 4: 76. DOI: 10.1038/s43586-024-00354-y.Peer-Reviewed Original ResearchChromatin tracingChromatin organizationHigh-throughput sequencing-based methodsRegulation of gene expressionSequencing-based methodsSingle-cellGenetic screening technologiesGenome foldingGenomic scaleGenome functionChromatin labelingGenomic levelSpectrum of cell typesDNA replicationModel organismsChromatinGene expressionIntact cellsSystematic profilingSingle-molecule levelCell typesGenomeScreening technologiesFilling major gapsPrimers
2021
Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture
Lu Y, Liu M, Yang J, Weissman SM, Pan X, Katz SG, Wang S. Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture. Cell Discovery 2021, 7: 47. PMID: 34183665, PMCID: PMC8238952, DOI: 10.1038/s41421-021-00266-1.Peer-Reviewed Original ResearchWild typeCell typesHSC nicheMultiplexed error-robust fluorescenceStem cell niche architectureFetal liverHematopoietic stem cell nicheStem cell nicheLoss of TET2Endothelial cellsBioinformatic foundationNumber of HSCsNiche architectureTranscriptome profilingSpatial regulationTranscriptional profilesCell nicheArterial endothelial cellsIndividual cellsNicheSitu hybridizationSpatial organizationLiver cell typesMicroenvironment regulationRobust fluorescenceChromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue
Liu M, Yang B, Hu M, Radda JSD, Chen Y, Jin S, Cheng Y, Wang S. Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. Nature Protocols 2021, 16: 2667-2697. PMID: 33903756, PMCID: PMC9007104, DOI: 10.1038/s41596-021-00518-0.Peer-Reviewed Original ResearchConceptsSame single cellNucleome architecturesGene expressionMammalian tissuesChromatin foldingNuclear laminaSingle cellsNumerous RNA speciesDifferent biological processesSingle mammalian cellsDifferent cell typesMultiplexed imagingGenomic organizationGenomic architectureChromatin loopsGenomic regionsRNA speciesIndividual chromosomesMammalian cellsGenomic techniquesBiological processesDetailed protocolCopy numberCell typesNormal development
2020
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
Liu M, Lu Y, Yang B, Chen Y, Radda JSD, Hu M, Katz SG, Wang S. Multiplexed imaging of nucleome architectures in single cells of mammalian tissue. Nature Communications 2020, 11: 2907. PMID: 32518300, PMCID: PMC7283333, DOI: 10.1038/s41467-020-16732-5.Peer-Reviewed Original ResearchConceptsNucleome architecturesChromatin organizationMammalian tissuesNumerous RNA speciesNumerous genomic regionsSpecific chromatin architectureSurface of chromosomesSingle cellsDifferent cell typesMouse fetal liverChromatin architectureMultiplexed imagingChromatin loopsChromatin foldingGenomic functionsNuclear laminaGenomic regionsRNA speciesMultiple genomesGene expressionCopy numberCell typesDe novoGenomeSame cells