GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE186918 Query DataSets for GSE186918
Status Public on Mar 01, 2022
Title ATACseq of CFBE41o- stably expressing wild-type CFTR (WTBE) and F508del-CFTR (CFBE) cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Cystic fibrosis (CF) is characterized by chronic inflammation and excessive cytokines secretion in the lung. Isogenic human CF bronchial epithelial (CFBE41o-) cell lines stably expressing wt-CFTR (WTBE) or F508del mutant (CFBE) are widely used tools in understanding responses to stimuli or drugs and CF pathogenesis in vitro. However, their intrinsic cellular differences in culture are unknown. Hence, we performed integrative analyses at protein, mRNA and chromatin levels on these isogenic cell lines cultured in submerged and transwell condition. CFBE and WTBE cells displayed different secretion patterns on IL-6, IL-8, CXCL1, CXCL10, and CCL5 . The ALI culture dramatically increased cytokines secretion in both cells. ATAC-seq results showed that CFBE cells exhibited higher genome-wide chromatin accessibility than WTBE cells in both culture methods, but the relative openness of cytokine genes between two cells varied individually. Differentially expressed genes between two cell lines from mRNA sequencing were highly concentrated in immunity-related pathways. While the mRNA stability of CXCL10 and CXCL1 exhibited the most significant differences between cell lines in SUB culture, most cytokines had comparable mRNA stabilities within same culture method. Moreover, polarization of cells via transwell culture remodeled the chromatin accessibility and transcriptome. This multilayered studies presents a comprehensive baseline activities of CFBE and WTBE cells, further facilitating their usage and data interpretation as CF cell models.
Overall design Chromatin-accessibility profile of WTBE and CFBE cells under different culture models.
Contributor(s) Kolls JK, Lu S, Song K
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 01, 2021
Last update date Mar 01, 2022
Contact name Jay Kolls
Organization name Tulane University
Department Medicine
Lab Center for Translational Research in Infection and Inflammation
Street address 1430 Tulane Ave
City New Orleans
State/province LA
ZIP/Postal code 70112
Country USA
Platforms (2)
GPL21697 NextSeq 550 (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (12)
GSM5663712 WTBE SUB rep1 (ATAC-seq)
GSM5663713 WTBE SUB rep2 (ATAC-seq)
GSM5663714 WTBE SUB rep3 (ATAC-seq)
This SubSeries is part of SuperSeries:
GSE186920 Multi-omics comparisons between CFBE41o- cells stably expressing wide-type CFTR and F508del-mutant CFTR
BioProject PRJNA776762
SRA SRP344019

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
GSE186918_ALI_callpeak.csv.gz 3.4 Mb (ftp)(http) CSV
GSE186918_SUB_callpeak.csv.gz 2.9 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap