2023
Generation of ventralized human thalamic organoids with thalamic reticular nucleus
Kiral F, Cakir B, Tanaka Y, Kim J, Yang W, Wehbe F, Kang Y, Zhong M, Sancer G, Lee S, Xiang Y, Park I. Generation of ventralized human thalamic organoids with thalamic reticular nucleus. Cell Stem Cell 2023, 30: 677-688.e5. PMID: 37019105, PMCID: PMC10329908, DOI: 10.1016/j.stem.2023.03.007.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsSingle-cell RNA sequencingReceptor tyrosine protein kinaseTyrosine protein kinaseEmbryonic stem cellsDisease-associated genesLineage developmentRNA sequencingHuman brain developmentOrganoid systemsStem cellsHuman brain organoidsNeuronal functionBrain organoidsOrganoidsBrain organoid systemsDistinct nucleiBrain developmentThalamic developmentPTCHD1NucleusKinaseGenesSequencing
2017
Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells
Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Research 2017, 45: e77-e77. PMID: 28126923, PMCID: PMC5605247, DOI: 10.1093/nar/gkx026.Peer-Reviewed Original ResearchMeSH KeywordsCell LineCell Line, TumorChromosome MappingCpG IslandsDNA MethylationDNA Restriction EnzymesEpigenesis, GeneticFibroblastsGenetic VariationGenome, HumanHigh-Throughput Nucleotide SequencingHumansInduced Pluripotent Stem CellsK562 CellsLymphocytesPromoter Regions, GeneticSingle-Cell AnalysisConceptsSingle cellsMethylation-sensitive restriction enzyme digestionCpG methylation patternsDNA bisulfite sequencingInduced pluripotent stem cellsSingle-cell levelCpG island methylationPluripotent stem cellsHeterogeneous cell populationsMultiple displacement amplificationEpigenetic heterogeneityMethylation sequencingBisulfite sequencingENCODE dataMethylation patternsMethylation differencesMethylation profilesRestriction enzyme digestionIsland methylationIndividual cellsHematopoietic cellsStem cellsSmall populationSequencingEnzyme digestion
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 procedure
2009
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming
Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, Zhang K. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology 2009, 27: 353-360. PMID: 19330000, PMCID: PMC2715272, DOI: 10.1038/nbt.1530.Peer-Reviewed Original ResearchConceptsHuman CpG islandsLarge eukaryotic genomesStem cellsEmbryonic stem cellsWhole-genome analysisPluripotent stem cellsEukaryotic genomesNuclear reprogrammingCytosine methylationBisulfite sequencingDNA methylationCpG islandsMethylationPadlock probesGenomeCellsReprogrammingSequencingFibroblastsIslandsTargeted and genome-scale strategies reveal gene-body methylation signatures in human cells
Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature Biotechnology 2009, 27: 361-368. PMID: 19329998, PMCID: PMC3566772, DOI: 10.1038/nbt.1533.Peer-Reviewed Original Research