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| Status |
Public on Jun 07, 2023 |
| Title |
Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts [4C-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| 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.
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| Overall design |
Analysis of the 3D chromatin architecture with 4C-seq at the CFTR locus to determine interaction frequencies between elements in 16HBE14o- CFTR-high vs 16HBE14o- CFTR-low cells
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| 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 |
| E-mail(s) |
axh575@case.edu
|
| Organization name |
Case Western Reserve University
|
| Department |
Genetics and Genome Sciences
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| Street address |
2109 Adelbert Rd
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
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| Platforms (1) |
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| Samples (18)
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| GSM6822462 |
16HBE14o- viewpoint_+48.9kb [4C-seq] |
| GSM6822463 |
16HBE14o- viewpoint_-20.9kb [4C-seq] |
| GSM6822464 |
16HBE14o- CFTRhigh #4 viewpoint_+48.9kb rep1 [4C-seq] |
| GSM6822465 |
16HBE14o- CFTRhigh #4 viewpoint_+48.9kb rep2 [4C-seq] |
| GSM6822466 |
16HBE14o- CFTRhigh #4 viewpoint_-20.9kb rep1 [4C-seq] |
| GSM6822467 |
16HBE14o- CFTRhigh #4 viewpoint_-20.9kb rep2 [4C-seq] |
| GSM6822468 |
16HBE14o- CFTRhigh #7 viewpoint_+48.9kb rep1 [4C-seq] |
| GSM6822469 |
16HBE14o- CFTRhigh #7 viewpoint_+48.9kb rep2 [4C-seq] |
| GSM6822470 |
16HBE14o- CFTRhigh #7 viewpoint_-20.9kb rep1 [4C-seq] |
| GSM6822471 |
16HBE14o- CFTRhigh #7 viewpoint_+-20.9kb rep2 [4C-seq] |
| GSM6822472 |
16HBE14o- CFTRlow #3 viewpoint_+48.9kb rep1 [4C-seq] |
| GSM6822474 |
16HBE14o- CFTRlow #3 viewpoint_+48.9kb rep2 [4C-seq] |
| GSM6822475 |
16HBE14o- CFTRlow #3 viewpoint_-20.9kb rep1 [4C-seq] |
| GSM6822476 |
16HBE14o- CFTRlow #3 viewpoint_-20.9kb rep2 [4C-seq] |
| GSM6822477 |
16HBE14o- CFTRlow #12 viewpoint_+48.9kb rep1 [4C-seq] |
| GSM6822478 |
16HBE14o- CFTRlow #12 viewpoint_+48.9kb rep2 [4C-seq] |
| GSM6822479 |
16HBE14o- CFTRlow #12 viewpoint_-20.9kb rep1 [4C-seq] |
| GSM6822480 |
16HBE14o- CFTRlow #12 viewpoint_-20.9kb rep2 [4C-seq] |
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| This SubSeries is part of SuperSeries: |
| GSE220855 |
Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts. |
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| Relations |
| BioProject |
PRJNA911927 |
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