2024
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Farzad N, Enninful A, Bao S, Zhang D, Deng Y, Fan R. Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nature Protocols 2024, 19: 3389-3425. PMID: 38943021, DOI: 10.1038/s41596-024-01013-y.Peer-Reviewed Original ResearchTn5 transpositionDeterministic barcodingGenome-wide profiling of histone modificationsProfiling of histone modificationsTransposase-accessible chromatin sequencingEpigenomic profiling methodsGenome-wide profilingSingle-base resolutionGene regulation programsGenomic DNA locusNext-generation sequencingDNA lociBioinformatics skillsLibrary preparationDNA barcodingChromatin accessibilityChromatin sequencingHistone modificationsEpigenome sequencingEpigenetic landscapeEpigenetic mapsCellular functionsEpigenetic markersCustom pipelineBarcoding
2023
Spatial epigenome–transcriptome co-profiling of mammalian tissues
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija G, Dwork A, Mann J, Leong K, Boldrini M, Wang L, Haeussler M, Raphael B, Kluger Y, Castelo-Branco G, Fan R. Spatial epigenome–transcriptome co-profiling of mammalian tissues. Nature 2023, 616: 113-122. PMID: 36922587, PMCID: PMC10076218, DOI: 10.1038/s41586-023-05795-1.Peer-Reviewed Original ResearchConceptsGene expressionSingle-cell resolutionChromatin accessibilityJoint profilingHistone modificationsGene regulationCellular statesEpigenetic mechanismsCentral dogmaSpatial transcriptomeTranscriptional phenotypeCell statesOmics informationSpatial transcriptomicsEpigenetic primingMammalian tissuesEpigenomeMolecular biologyTissue architectureCell dynamicsMechanistic relationshipDifferential rolesNew insightsMouse brainProfiling