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
2020
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue
Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Cell 2020, 183: 1665-1681.e18. PMID: 33188776, PMCID: PMC7736559, DOI: 10.1016/j.cell.2020.10.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutomationBrainCluster AnalysisDNA Barcoding, TaxonomicDNA, ComplementaryEmbryo, MammalianEyeFemaleGene Expression Regulation, DevelopmentalGenomicsHuman Umbilical Vein Endothelial CellsHumansMice, Inbred C57BLMicrofluidicsOrgan SpecificityReproducibility of ResultsRNA, MessengerSingle-Cell AnalysisTranscriptomeConceptsDeterministic barcodingNext-generation sequencingSingle-cell transcriptomesGene expression profilesMajor tissue typesDBiT-seqDNA barcodesDevelopmental biologyExpression profilesEarly organogenesisCancer biologyCell typesBarcodingTissue typesSequencingBarcodesBiologyRapid identificationSets of barcodesTranscriptomeParallel microfluidic channelsOrganogenesisEmbryosProteinTissue pixels
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