2018
Transcriptome and epigenome landscape of human cortical development modeled in organoids
Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM, Gerstein M, Crawford G, Sestan N, Abyzov A, Vaccarino F, Akbarian S, An J, Armoskus C, Ashley-Koch A, Beach T, Belmont J, Bendl J, Borrman T, Brown L, Brown M, Brown M, Brunetti T, Bryois J, Burke E, Camarena A, Carlyle B, Chae Y, Charney A, Chen C, Cheng L, Cherskov A, Choi J, Clarke D, Collado-Torres L, Dai R, De La Torre Ubieta L, DelValle D, Devillers O, Dracheva S, Emani P, Evgrafov O, Farnham P, Fitzgerald D, Flatow E, Francoeur N, Fullard J, Gandal M, Gao T, Garrett M, Geschwind D, Giase G, Girdhar K, Giusti-Rodriguez P, Goes F, Goodman T, Grennan K, Gu M, Gürsoy G, Hadjimichael E, Hahn C, Haroutunian V, Hauberg M, Hoffman G, Huey J, Hyde T, Ivanov N, Jacobov R, Jaffe A, Jiang Y, Jiang Y, Johnson G, Kassim B, Kefi A, Kim Y, Kitchen R, Kleiman J, Knowles J, Kozlenkov A, Li M, Li Z, Lipska B, Liu C, Liu S, Mangravite L, Mariani J, Mattei E, Miller D, Moore J, Nairn A, Navarro F, Park R, Peters M, Pinto D, Pochareddy S, Polioudakis D, Pratt H, Price A, Purcaro M, Ray M, Reddy T, Rhie S, Roussos P, Sanders S, Santpere G, Schreiner S, Sheppard B, Shi X, Shieh A, Shin J, Skarica M, Song L, Sousa A, Spitsyna V, State M, Sullivan P, Swarup V, Szatkiewicz J, Szekely A, Tao R, van Bakel H, Wang Y, Wang D, Warrell J, Webster M, Weissman S, Weng Z, Werling D, White K, Willsey J, Wiseman J, Witt H, Won H, Wray G, Xia Y, Xu M, Yang Y, Yang M, Zandi P, Zhang J, Zharovsky E. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science 2018, 362 PMID: 30545853, PMCID: PMC6426303, DOI: 10.1126/science.aat6720.Peer-Reviewed Original ResearchCerebral CortexEnhancer Elements, GeneticEpigenesis, GeneticGene Expression Regulation, DevelopmentalHumansInduced Pluripotent Stem CellsModels, NeurologicalNeurogenesisOrganoidsTranscriptomeIntegrative functional genomic analysis of human brain development and neuropsychiatric risks
Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw C, Pardiñas AF, Hu M, Jin F, Li Y, Owen M, O’Donovan M, Walters J, Posthuma D, Reimers M, Levitt P, Weinberger D, Hyde T, Kleinman J, Geschwind D, Hawrylycz M, State M, Sanders S, Sullivan P, Gerstein M, Lein E, Knowles J, Sestan N, Willsey A, Oldre A, Szafer A, Camarena A, Cherskov A, Charney A, Abyzov A, Kozlenkov A, Safi A, Jones A, Ashley-Koch A, Ebbert A, Price A, Sekijima A, Kefi A, Bernard A, Amiri A, Sboner A, Clark A, Jaffe A, Tebbenkamp A, Sodt A, Guillozet-Bongaarts A, Nairn A, Carey A, Huttner A, Chervenak A, Szekely A, Shieh A, Harmanci A, Lipska B, Carlyle B, Gregor B, Kassim B, Sheppard B, Bichsel C, Hahn C, Lee C, Chen C, Kuan C, Dang C, Lau C, Cuhaciyan C, Armoskus C, Mason C, Liu C, Slaughterbeck C, Bennet C, Pinto D, Polioudakis D, Franjic D, Miller D, Bertagnolli D, Lewis D, Feng D, Sandman D, Clarke D, Williams D, DelValle D, Fitzgerald D, Shen E, Flatow E, Zharovsky E, Burke E, Olson E, Fulfs E, Mattei E, Hadjimichael E, Deelman E, Navarro F, Wu F, Lee F, Cheng F, Goes F, Vaccarino F, Liu F, Hoffman G, Gürsoy G, Gee G, Mehta G, Coppola G, Giase G, Sedmak G, Johnson G, Wray G, Crawford G, Gu G, van Bakel H, Witt H, Yoon H, Pratt H, Zhao H, Glass I, Huey J, Arnold J, Noonan J, Bendl J, Jochim J, Goldy J, Herstein J, Wiseman J, Miller J, Mariani J, Stoll J, Moore J, Szatkiewicz J, Leng J, Zhang J, Parente J, Rozowsky J, Fullard J, Hohmann J, Morris J, Phillips J, Warrell J, Shin J, An J, Belmont J, Nyhus J, Pendergraft J, Bryois J, Roll K, Grennan K, Aiona K, White K, Aldinger K, Smith K, Girdhar K, Brouner K, Mangravite L, Brown L, Collado-Torres L, Cheng L, Gourley L, Song L, Ubieta L, Habegger L, Ng L, Hauberg M, Onorati M, Webster M, Kundakovic M, Skarica M, Reimers M, Johnson M, Chen M, Garrett M, Sarreal M, Reding M, Gu M, Peters M, Fisher M, Gandal M, Purcaro M, Smith M, Brown M, Shibata M, Brown M, Xu M, Yang M, Ray M, Shapovalova N, Francoeur N, Sjoquist N, Mastan N, Kaur N, Parikshak N, Mosqueda N, Ngo N, Dee N, Ivanov N, Devillers O, Roussos P, Parker P, Manser P, Wohnoutka P, Farnham P, Zandi P, Emani P, Dalley R, Mayani R, Tao R, Gittin R, Straub R, Lifton R, Jacobov R, Howard R, Park R, Dai R, Abramowicz S, Akbarian S, Schreiner S, Ma S, Parry S, Shapouri S, Weissman S, Caldejon S, Mane S, Ding S, Scuderi S, Dracheva S, Butler S, Lisgo S, Rhie S, Lindsay S, Datta S, Souaiaia T, Roychowdhury T, Gomez T, Naluai-Cecchini T, Beach T, Goodman T, Gao T, Dolbeare T, Fliss T, Reddy T, Chen T, Hyde T, Brunetti T, Lemon T, Desta T, Borrman T, Haroutunian V, Spitsyna V, Swarup V, Shi X, Jiang Y, Xia Y, Chen Y, Jiang Y, Wang Y, Chae Y, Yang Y, Kim Y, Riley Z, Krsnik Z, Deng Z, Weng Z, Lin Z, Li Z. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 2018, 362 PMID: 30545854, PMCID: PMC6413317, DOI: 10.1126/science.aat7615.Peer-Reviewed Original ResearchMeSH KeywordsBrainEpigenesis, GeneticEpigenomicsGene Expression Regulation, DevelopmentalGene Regulatory NetworksHumansMental DisordersNervous System DiseasesNeurogenesisSingle-Cell AnalysisTranscriptomeConceptsIntegrative functional genomic analysisFunctional genomic analysisCell typesGene coexpression modulesDistinct cell typesCell type-specific dynamicsGenomic basisEpigenomic reorganizationEpigenomic landscapeEpigenomic regulationGenomic analysisCoexpression modulesIntegrative analysisHuman brain developmentFetal transitionHuman neurodevelopmentGenetic associationCellular compositionNeuropsychiatric riskBrain developmentNeurodevelopmental processesGenesTraitsPostnatal developmentNeuropsychiatric disorders
2001
TARPP, a novel protein that accompanies TCR gene rearrangement and thymocyte education
Kisielow J, Nairn A, Karjalainen K. TARPP, a novel protein that accompanies TCR gene rearrangement and thymocyte education. European Journal Of Immunology 2001, 31: 1141-1149. PMID: 11298339, DOI: 10.1002/1521-4141(200104)31:4<1141::aid-immu1141>3.0.co;2-r.Peer-Reviewed Original ResearchAgingAmino Acid SequenceAnimalsAntibodiesBase SequenceCD3 ComplexCell DifferentiationCell LineageCells, CulturedCloning, MolecularDown-RegulationFlow CytometryGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Rearrangement, T-LymphocyteMiceMice, Inbred C57BLMolecular Sequence DataMolecular WeightPhosphoproteinsProtein Phosphatase 1Receptors, Antigen, T-CellRNA, MessengerSignal TransductionThymus Gland
1997
Widespread Neuronal Ectopia Associated with Secondary Defects in Cerebrocortical Chondroitin Sulfate Proteoglycans and Basal Lamina in MARCKS-Deficient Mice
Blackshear P, Silver J, Nairn A, Sulik K, Squier M, Stumpo D, Tuttle J. Widespread Neuronal Ectopia Associated with Secondary Defects in Cerebrocortical Chondroitin Sulfate Proteoglycans and Basal Lamina in MARCKS-Deficient Mice. Experimental Neurology 1997, 145: 46-61. PMID: 9184108, DOI: 10.1006/exnr.1997.6475.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodies, MonoclonalBasement MembraneCerebral CortexChondroitin SulfatesFemaleGene Expression Regulation, DevelopmentalIntracellular Signaling Peptides and ProteinsLamininMaleMembrane ProteinsMiceMice, Mutant StrainsMicroscopy, Electron, ScanningMutationMyristoylated Alanine-Rich C Kinase SubstrateNeurogliaNeuronsPia MaterPregnancyProteinsProteoglycansReticulinSynaptophysinConceptsChondroitin sulfate proteoglycanNeuronal ectopiaBasal laminaSulfate proteoglycanProtein kinase CEmbryonic day 13Basal lamina proteinsReticulin stainingSubarachnoid spaceForebrain commissuresPial membraneDay 13EctopiaGross abnormalitiesRetinal laminationMiceMARCKS deficiencyAbnormalitiesPotential mechanismsNeural substratesMarginal zoneProteolytic destructionKinase CProteoglycansLamina
1996
Developmental expression of MARCKS and protein kinase C in mice in relation to the exencephaly resulting from MARCKS deficiency
Blackshear P, Lai W, Tuttle J, Stumpo D, Kennington E, Nairn A, Sulik K. Developmental expression of MARCKS and protein kinase C in mice in relation to the exencephaly resulting from MARCKS deficiency. Brain Research 1996, 96: 62-75. PMID: 8922669, DOI: 10.1016/0165-3806(96)00097-1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBeta-GalactosidaseEmbryonic and Fetal DevelopmentGene Expression Regulation, DevelopmentalGene Expression Regulation, EnzymologicImmunohistochemistryIntracellular Signaling Peptides and ProteinsIsoenzymesMembrane ProteinsMiceMice, Inbred C57BLMice, TransgenicMyristoylated Alanine-Rich C Kinase SubstrateNerve Tissue ProteinsNeural Tube DefectsPhosphorylationProtein Kinase CProteinsRecombinant Fusion ProteinsConceptsProtein kinase CNeural tube closureKinase CPlasma membraneTube closureNeural tubeCranial neural tube closureMajor cellular substrateEmbryonic day 8.5MARCKS deficiencySpecific cell typesE8.5 embryosCranial neural tubeMouse geneFunctional defectsMARCKS proteinPerinatal lethalityMARCKSCellular substratesCranial neurulationMARCKS expressionUnderlying mesenchymeDevelopmental expressionPKC-alphaDay 8.5