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Series GSE46194 Query DataSets for GSE46194
Status Public on May 07, 2013
Title Multiple roles for Grainyhead-like transcription factors in the establishment and maintenance of human mucociliary airway epithelium (ChIP-Seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated p63+ Krt5+ basal cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in co-ordinating the expression of numerous proteins required for epithelial morphogenesis, differentiation, remodeling and repair. However, little is known about their function in the adult lung. Here, we focus on the role of GRHL2 in primary human bronchial epithelial (HBE) cells, using either shRNA or a dominant negative protein (DN-GRHL2) to inhibit its function. We follow changes in epithelial phenotype, and in gene transcription using RNA-seq or microarray analysis, both in undifferentiated basal cells and in cells differentiating in air-liquid interface culture into a mucociliary epithelium with transepithelial electrical resistance. We identify several hundreds of genes that are directly or indirectly regulated by GRHL2. Using ChIP-seq to map sites of GRHL2 binding in the basal cells we identify 7,687 potential primary targets, and confirm that GRHL2 binding is strongly enriched near GRHL-regulated genes. Different subsets of the large cohort of potential GRHL2 targets appear to be active in basal and differentiated cells. Taken together, the results strongly support the hypothesis that GRHL2 plays a key role in regulating many physiological functions of human airway epithelium, including those involving cell adhesion, polarity and morphogenesis.
 
Overall design Frozen primary human bronchial epithelial (HBE) cells were obtained from three donors and grown to confluence in standard culture conditions. Cells were crosslinked with formaldehyde and collected in aliquots of ~20M cells per donor. ChIP-seq for GRHL2 (Antibody: Sigma HPA004820) was then performed relative to an input control for each donor.
 
Contributor(s) Gao X, Vockley CM, Pauli F, Newberry KM, Xue Y, Randell SH, Reddy TE, Hogan BL
Citation(s) 23690579
Submission date Apr 18, 2013
Last update date Mar 20, 2019
Contact name Timothy E Reddy
E-mail tim.reddy@duke.edu
Organization name Duke University
Department Department of Biostatistics & Bioinformatics
Lab ReddyLab
Street address 2347 CIEMAS, 101 Science Drive
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (6)
GSM1125982 C_29_GRHL2_ChIPseq
GSM1125983 C_36_GRHL2_ChIPseq
GSM1125984 C_44_GRHL2_ChIPseq
Relations
BioProject PRJNA198009
SRA SRP021180

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE46194_RAW.tar 100.2 Mb (http)(custom) TAR (of BEDGRAPH)
Raw data are available in SRA
Processed data provided as supplementary file

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