2016
Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors
Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Nucleic Acids Research 2016, 45: 1281-1296. PMID: 28003475, PMCID: PMC5388401, DOI: 10.1093/nar/gkw1214.Peer-Reviewed Original ResearchConceptsHematopoietic stem cellsPrecursor cellsInduction of anemiaInterferon response genesG2/M phaseEarly precursor cellsHomeostatic cellsStages of differentiationTranscription factorsSurface markersCell cycle progressionLong-term hematopoietic stem cellsSpecific augmentationAnemic miceMarked increaseEarly hematopoietic precursorsHematopoietic precursorsStem cellsCycle progressionM phaseSingle-cell transcriptomicsCellsCell differentiationHematopoietic stressLineage-specific transcription factors
2013
Notch-HES1 signaling axis controls hemato-endothelial fate decisions of human embryonic and induced pluripotent stem cells
Lee JB, Werbowetski-Ogilvie TE, Lee JH, McIntyre BA, Schnerch A, Hong SH, Park IH, Daley GQ, Bernstein ID, Bhatia M. Notch-HES1 signaling axis controls hemato-endothelial fate decisions of human embryonic and induced pluripotent stem cells. Blood 2013, 122: 1162-1173. PMID: 23733337, DOI: 10.1182/blood-2012-12-471649.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisBasic Helix-Loop-Helix Transcription FactorsBiomarkersBlotting, WesternCell DifferentiationCell MovementCell ProliferationCells, CulturedDermisEmbryonic Stem CellsEndothelium, VascularFibroblastsFlow CytometryGene Expression ProfilingGene Expression RegulationHematopoiesisHematopoietic Stem CellsHomeodomain ProteinsHumansImmunoenzyme TechniquesInduced Pluripotent Stem CellsOligonucleotide Array Sequence AnalysisReceptor, Notch1Receptors, NotchRNA, Small InterferingSignal TransductionTranscription Factor HES-1ConceptsCell fate decisionsFate decisionsPluripotent stem cellsHematopoietic lineage specificationEarly human hematopoiesisFunction of NotchStem cellsHuman pluripotent stem cellsInduced pluripotent stem cellsRole of NotchEarly human developmentCommitted hematopoietic progenitorsFate specificationLineage specificationCellular processesNotch receptorsNotch signalingHematopoietic lineagesNotch pathwayBipotent precursorsNotch ligandsHuman hematopoiesisHuman embryonicUnappreciated roleToggle switchTransformation of somatic cells into stem cell‐like cells under a stromal niche
Lee ST, Gong SP, Yum KE, Lee EJ, Lee CH, Choi JH, Kim DY, Han H, Kim K, Hysolli E, Ahn JY, Park I, Han JY, Jeong J, Lim JM. Transformation of somatic cells into stem cell‐like cells under a stromal niche. The FASEB Journal 2013, 27: 2644-2656. PMID: 23580613, PMCID: PMC4050423, DOI: 10.1096/fj.12-223065.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell AggregationCell DedifferentiationCell FusionCells, CulturedChromosome AberrationsCoculture TechniquesEmbryo, MammalianEmbryonic Stem CellsFemaleFibroblastsGene Expression ProfilingInduced Pluripotent Stem CellsKaryotypingMiceMice, Inbred C57BLMice, Inbred CBAMice, Inbred DBAMice, Inbred ICRMicroscopy, Electron, TransmissionOligonucleotide Array Sequence AnalysisOvarySpecies SpecificityStem Cell NicheStem CellsConceptsEmbryonic stem cellsColony-forming fibroblastsParthenogenetic embryonic stem cellsSomatic cellsGenomic single nucleotide polymorphismsAcquisition of pluripotencySomatic cell plasticityPluripotency gene expressionStem cellsInner cell massStem cell-like cellsCell cycle-related proteinsPluripotent stem cellsSomatic genomeCycle-related proteinsGenomic plasticityCell-like cellsSingle nucleotide polymorphismsCell plasticityESC coloniesGenetic manipulationHeterologous recombinationEmbryonic fibroblastsImprinting patternGene expression
2012
Two methods for full-length RNA sequencing for low quantities of cells and single cells
Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, LaMotte RH, Park IH, Snyder MP, Mason CE, Weissman SM. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 110: 594-599. PMID: 23267071, PMCID: PMC3545756, DOI: 10.1073/pnas.1217322109.Peer-Reviewed Original ResearchConceptsRNA sequencingSingle cellsFull-length RNA sequencingSingle dorsal root ganglion neuronHigh-throughput sequencingGene expression patternsLower transcript levelsFull-length sequencesRandom oligonucleotide primersTranscript representationAbundant mRNAsK562 erythroleukemic cellsTranscript levelsMRNA sequencingExpression patternsBiological disciplinesErythroleukemic cellsExpression signaturesSequencingOligonucleotide primersFull lengthLow quantitiesDNA amplificationRNAPCR procedureAltered hematopoiesis in trisomy 21 as revealed through in vitro differentiation of isogenic human pluripotent cells
MacLean GA, Menne TF, Guo G, Sanchez DJ, Park IH, Daley GQ, Orkin SH. Altered hematopoiesis in trisomy 21 as revealed through in vitro differentiation of isogenic human pluripotent cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 17567-17572. PMID: 23045682, PMCID: PMC3491455, DOI: 10.1073/pnas.1215468109.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationDown SyndromeGene Expression ProfilingHematopoiesisHumansKaryotypingPluripotent Stem CellsPolymerase Chain ReactionConceptsHuman embryonic stemPluripotent cellsHuman pluripotent cellsFetal liver stageEffects of trisomyPluripotent stem cellsDefinitive hematopoiesisIsogenic originColony-forming potentialColony-forming assaysΓ-globinEmbryonic stemIPS linesDifferentiation conditionsAltered hematopoiesisClonal variationHematopoietic cellsStem cellsHematopoiesisHematopoietic abnormalitiesChromosome 21Two- to fivefold increaseFetal liverTrisomic cellsMyeloid hematopoiesis
2010
MicroRNA Profiling Reveals Two Distinct p53-Related Human Pluripotent Stem Cell States
Neveu P, Kye MJ, Qi S, Buchholz DE, Clegg DO, Sahin M, Park IH, Kim KS, Daley GQ, Kornblum HI, Shraiman BI, Kosik KS. MicroRNA Profiling Reveals Two Distinct p53-Related Human Pluripotent Stem Cell States. Cell Stem Cell 2010, 7: 671-681. PMID: 21112562, DOI: 10.1016/j.stem.2010.11.012.Peer-Reviewed Original ResearchConceptsInduced pluripotent stem cellsPluripotent stem cell stateEmbryonic stem cellsStem cell stateCell statesDifferentiated cellsStem cellsCell linesPluripotent stem cellsHuman cell linesGene setsMiRNA expression levelsMiR-92Cell line originMicroRNA profilingCancer cell linesLine originMiRNA profilesExpression levelsPluripotencyCancer cellsMiR-141CellsSubtle differencesHESCs
2009
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nature Genetics 2009, 41: 1350-1353. PMID: 19881528, PMCID: PMC2958040, DOI: 10.1038/ng.471.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCpG IslandsDNA MethylationEmbryonic Stem CellsEpigenesis, GeneticFibroblastsGene Expression ProfilingHumansInduced Pluripotent Stem CellsNeoplasms
2008
Regulatory networks define phenotypic classes of human stem cell lines
Müller FJ, Laurent LC, Kostka D, Ulitsky I, Williams R, Lu C, Park IH, Rao MS, Shamir R, Schwartz PH, Schmidt NO, Loring JF. Regulatory networks define phenotypic classes of human stem cell lines. Nature 2008, 455: 401-405. PMID: 18724358, PMCID: PMC2637443, DOI: 10.1038/nature07213.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsArtificial IntelligenceCell DifferentiationCell LineComputational BiologyDatabases, FactualEmbryonic Stem CellsGene Expression ProfilingHumansMiceMultipotent Stem CellsOligonucleotide Array Sequence AnalysisOocytesPhenotypePluripotent Stem CellsProtein BindingStem CellsConceptsStem cell linesStem cellsCell linesCell typesProtein-protein networkHuman stem cell linesDifferent human cell linesSpecific molecular networksPluripotent stem cell lineHuman stem cellsHuman cell linesRegulatory networksTranscriptional profilesBioinformatics analysisPhenotypic classesMolecular networksNeural stem cell lineLimited repertoireTight controlCellsCell samplesPluripotencyEmbryosLinesBroad range
2007
Reprogramming of human somatic cells to pluripotency with defined factors
Park IH, Zhao R, West JA, Yabuuchi A, Huo H, Ince TA, Lerou PH, Lensch MW, Daley GQ. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 2007, 451: 141-146. PMID: 18157115, DOI: 10.1038/nature06534.Peer-Reviewed Original ResearchMeSH KeywordsAdultAnimalsCell DifferentiationCell ShapeCells, CulturedDNA MethylationDNA-Binding ProteinsEmbryonic Stem CellsFetusFibroblastsGene Expression ProfilingHMGB ProteinsHomeodomain ProteinsHumansInfant, NewbornKruppel-Like Factor 4Kruppel-Like Transcription FactorsMiceNanog Homeobox ProteinOctamer Transcription Factor-3Pluripotent Stem CellsPromoter Regions, GeneticProto-Oncogene Proteins c-mycSOXB1 Transcription FactorsTeratomaTranscription FactorsTransplantation, HeterologousConceptsEmbryonic stem cellsStem cellsIPS cellsHuman somatic cellsInduced pluripotent stem cellsHuman iPS cellsPluripotent stem cellsHuman primary cellsPatient-specific cellsEarly embryosTranscription factorsSomatic cellsEctopic expressionPluripotencyGene expressionHuman cellsMurine fibroblastsDefined factorsPrimary cellsCell linesDermal fibroblastsCellsInvaluable toolFibroblastsExpression