Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification of early targets of SOX2 and PI3K signaling in normal, patient-derived tracheal basal cell lines.

ABSTRACT: Microarrays were used to examine gene expression changes in patient derived tracheal basal cell lines after treatment with Lenti-SOX2. Comparisons were made between baseline, Lenti-SOX2 and Lenti-SOX2 with a PI3K inhibitor (BKM120). Total RNA obtained from celll lnes 36 hours post lentivirus addition.

ORGANISM(S): Homo sapiens

SUBMITTER: carl virtanen

PROVIDER: E-GEOD-59866 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Distal cell-type-specific regulatory elements may be located at very large distances from the genes that they control and are often hidden within intergenic regions or in introns of other genes. The development of methods that enable mapping of regions of open chromatin genome wide has greatly advanced the identification and characterisation of these elements. Here we use DNase I hypersensitivity mapping followed by deep sequencing (DNase-seq) to generate a map of open chromatin in primary human tracheal epithelial (HTE) cells and use bioinformatic approaches to characterise the distribution of these sites within the genome and with respect to gene promoters, intronic and intergenic regions. Genes with THE-selective open chromatin at their promoters were associated with multiple pathways of epithelial function and differentiation. The data predict novel cell-type-specific regulatory elements for genes involved in HTE cell function, such as structural proteins and ion channels, and the transcription factors that may interact with them to control gene expression. Moreover, the map of open chromatin can identify the location of potentially critical regulatory elements in genome-wide association studies (GWAS) in which the strongest association is with single nucleotide polymorphisms in non-coding regions of the genome. We demonstrate its relevance to a recent GWAS that identifies modifiers of cystic fibrosis lung disease severity. Since HTE cells have many functional similarities with bronchial epithelial cells and other differentiated cells in the respiratory epithelium, these data are of direct relevance to elucidating the molecular basis of normal lung function and lung disease. HTE (human tracheal epithelial) cells were isolated from human trachea postmortem and grown as described previously (Davis P.B. et al.1990). Total RNA was extracted by Trizol and the samples shipped to NimbleGen for gene expression analysis on NimbleGen 4 X 72K HG18 60mer arrays.

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Identification of early targets of SOX2 and PI3K signaling in normal, patient-derived tracheal basal cell lines.

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