2024
Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues
Bai Z, Zhang D, Gao Y, Tao B, Zhang D, Bao S, Enninful A, Wang Y, Li H, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu M, Fan R. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell 2024 PMID: 39353436, DOI: 10.1016/j.cell.2024.09.001.Peer-Reviewed Original ResearchRNA biologyWhole-transcriptome sequencingMicroRNA regulatory networkSplicing dynamicsDeterministic barcodingRNA speciesRNA processingRNA variantsFFPE tissuesRegulatory networksTranscriptome sequencingSpliced isoformsNon-malignant cellsTumor clonal architecturesClonal architectureGene expressionCellular dynamicsRNAArchival formalin-fixed paraffin-embedded tissueMalignant subclonesFormalin-fixed paraffin-embedded (FFPEFFPE samplesParaffin-embedded (FFPEBiologyHuman lymphomas
2023
Microtechnologies for single-cell and spatial multi-omics
Deng Y, Bai Z, Fan R. Microtechnologies for single-cell and spatial multi-omics. Nature Reviews Bioengineering 2023, 1: 769-784. DOI: 10.1038/s44222-023-00084-y.Peer-Reviewed Original ResearchSuch single-cell dataGene regulatory networksMulti-omics assaysSingle-cell dataMulti-omics studiesSingle cellsContext of tissuesGenome scaleRegulatory networksOmics informationGene expressionOmics assaysCellular profilingSubcellular levelIntact tissueCellsFunctional stateAssaysOmicsMicroarrayTissueProfilingRegulationExpressionMicrofluidic platformSpatial 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