2025
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq
Li H, Bao S, Farzad N, Qin X, Fung A, Zhang D, Bai Z, Tao B, Fan R. Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq. Nature Protocols 2025, 1-35. PMID: 40119005, DOI: 10.1038/s41596-025-01145-9.Peer-Reviewed Original ResearchNear single-cell resolutionControl cell identityTargeting histone modificationsSingle-cell resolutionTn5 transposaseAccessible chromatinEpigenomic landscapeIn situ reverse transcriptionHistone modificationsCell identityTranscriptomic landscapeSequencing protocolSequencing methodsGene transcriptionEpigenomeOligonucleotide barcodesTranscriptomeDiverse biological activitiesIntact tissue sectionsReverse transcriptionTranscriptionBiological activityPrimary antibodyTagmentationTissue pixels
2023
The technological landscape and applications of single-cell multi-omics
Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nature Reviews Molecular Cell Biology 2023, 24: 695-713. PMID: 37280296, PMCID: PMC10242609, DOI: 10.1038/s41580-023-00615-w.Peer-Reviewed Original ResearchConceptsSingle-cell multi-omics technologiesMulti-omics technologiesMolecular cell biology researchCell lineage tracingCell biology researchBioinformatics toolsLineage tracingOmics methodsCell statesBiology researchMathematical modellingCancer geneticsOmics modalitiesComputational methodsEpitranscriptomeEpigenomeTranscriptomeGenomeProteomeOmicsOptimization of throughputGeneticsArt methodsTranslational researchUniquenessSpatial 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
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