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Series GSE220853 Query DataSets for GSE220853
Status Public on Jun 07, 2023
Title Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts [ATAC-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The airway epithelial cell line, 16HBE14o-, is an important cell model for studying airway disease. 16HBE14o- cells were originally generated from primary human bronchial epithelial cells by SV40-mediated immortalization, a process that is associated with genomic instability through long-term culture. Here we explore the heterogeneity of these cells, with respect to expression of the cystic fibrosis transmembrane conductance regulator (CFTR) transcript and protein. We isolate clones of 16HBE14o- with stably higher and lower levels of CFTR in comparison to bulk 16HBE14o-, designated CFTRhigh and CFTRlow. Detailed characterization of the CFTR locus in these clones by ATAC-seq and 4C-seq showed open chromatin profiles and higher order chromatin structure that correlate with CFTR expression levels. . Transcriptomic profiling of CFTRhigh and CFTRlow cells showed that the CFTRhigh cells had an elevated inflammatory/ innate immune response phenotype. These results encourage caution in interpreting functional data from clonal lines of 16HBE14o- cells, generated after genomic or other manipulations.
Overall design ATAC-seq to examine open chromatin in single cell clones isolated from bulk 16HBE14o- cells
Contributor(s) Kerschner JL, Paranjapye A, Harris A
Citation(s) 37269165
Submission date Dec 13, 2022
Last update date Jun 08, 2023
Contact name Ann Harris
Organization name Case Western Reserve University
Department Genetics and Genome Sciences
Street address 2109 Adelbert Rd
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (8)
GSM6822484 16HBE14o- CFTRhigh #4 rep1 [ATAC-seq]
GSM6822485 16HBE14o- CFTRhigh #4 rep2 [ATAC-seq]
GSM6822486 16HBE14o- CFTRhigh #7 rep1 [ATAC-seq]
This SubSeries is part of SuperSeries:
GSE220855 Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts.
BioProject PRJNA911926

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Supplementary file Size Download File type/resource 498.4 Mb (ftp)(http) BW 471.7 Mb (ftp)(http) BW
GSE220853_RAW.tar 1.9 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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