2020
Functional genomics analysis of human colon organoids identifies key transcription factors
Yin S, Ray G, Kerschner JL, Hao S, Perez A, Drumm ML, Browne JA, Leir SH, Longworth M, Harris A. Functional genomics analysis of human colon organoids identifies key transcription factors. Physiological Genomics 2020, 52: 234-244. PMID: 32390556, PMCID: PMC7311676, DOI: 10.1152/physiolgenomics.00113.2019.Peer-Reviewed Original ResearchConceptsHuman intestinal organoidsOpen chromatinTranscription factorsOpen chromatin profilesGenome-wide analysisFunctional genomic analysisCaudal type homeobox 2Open chromatin peaksKey transcription factorIntestinal epitheliumIntestinal epithelial differentiationChromatin profilesMolecular divergenceFunctional genomicsATAC-seqMotif analysisTranscriptome mappingGenomic analysisRNA-seqGenomic signaturesHuman colon organoidsFunctional overlapEpithelial transport processesType homeobox 2Organoid biology
2014
An Optimized Protocol for Isolating Primary Epithelial Cell Chromatin for ChIP
Browne JA, Harris A, Leir SH. An Optimized Protocol for Isolating Primary Epithelial Cell Chromatin for ChIP. PLOS ONE 2014, 9: e100099. PMID: 24971909, PMCID: PMC4074041, DOI: 10.1371/journal.pone.0100099.Peer-Reviewed Original ResearchConceptsCell typesChromatin immunoprecipitation dataDNA-binding proteinsLysis bufferPrimary human epithelial cellsEpithelial cell typesEpithelial cellsChromatin purificationHuman bronchial epithelial cellsENCODE consortiumHuman epithelial cellsCell chromatinNext-generation sequencingImmunoprecipitation dataCell lysis procedurePrimary human bronchial epithelial cellsChromatinFormaldehyde-fixed cellsBronchial epithelial cellsMembrane lysisSize selectionLysis procedureAdherent cellsCellsLysis step