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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 01, 2018 |
| Title |
A single cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The functions of epithelial tissues are dictated by the types, abundance, and distribution of the differentiated cells they contain. Attempts to restore tissue function after damage require knowledge of how physiological tasks are distributed among cell types, and how cell states vary between homeostasis, injury/repair, and disease. In the conducting airway, a heterogeneous basal cell population gives rise to specialized luminal cells that perform mucociliary clearance. We performed single cell profiling of human bronchial epithelial cells and mouse tracheal epithelial cells to obtain a comprehensive picture of cell types in the conducting airway and their behavior in homeostasis and regeneration. Our analysis reveals cell states that represent known and novel cell populations, delineates their heterogeneity, and identifies distinct differentiation trajectories during homeostasis and tissue repair. Finally, we identified a novel, rare cell type, which we call the "pulmonary ionocyte", that co-expresses FOXI1, multiple subunits of the V-ATPase, and CFTR, the gene mutated in cystic fibrosis (CF). Using immunofluorescence, signaling pathway modulation, and electrophysiology, we show that Notch signaling is necessary and FOXI1 expression sufficient to drive the production of the pulmonary ionocyte, and that the pulmonary ionocyte is a major source of CFTR activity in the conducting airway epithelium.
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| Overall design |
Single-cell mRNA sequencing of: a) primary mouse upper airway epithelial cells under homeostasis and in a recovery time course following polidocanol induced injury (14,163 cells); b) human bronchial epithelial cells (HBECs) growns in an air-liquid interface (ALI) culture (2,970 cells); c) HBECs transduced with GFP (9,436 cells) or GFP:FOXI1 (10,330 cells) and grown in an ALI culture.
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| Contributor(s) |
Plasschaert LW, Zilionis R, Choo-Wing R, Savova V, Knehr J, Roma G, Klein AM, Jaffe AB |
| Citation(s) |
30069046 |
| BioProject |
PRJNA396450 |
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| Submission date |
Aug 11, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Rapolas Zilionis |
| E-mail(s) |
rapolas.zilionis@bti.vu.lt
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| Organization name |
Vilnius University
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| Department |
Life Sciences Center
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| Lab |
Mazutis
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| Street address |
Sauletekis av 7
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| City |
Vilnius |
| State/province |
LT |
| ZIP/Postal code |
10257 |
| Country |
Lithuania |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (15)
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| GSM2741419 |
Uninjured trachea, mouse id 54, 1798 cells |
| GSM2741420 |
Uninjured trachea, mouse id 55, 1470 cells |
| GSM2741421 |
Uninjured trachea, mouse id 56, 2659 cells |
| GSM2741422 |
Uninjured trachea, mouse id 57, 1971 cells |
| GSM2741423 |
Trachea 24h post-injury by polidocanol, mouse id 59, 898 cells |
| GSM2741424 |
Trachea 48h post-injury by polidocanol, mouse id 61, 1964 cells |
| GSM2741425 |
Trachea 72h post-injury by polidocanol, mouse id 65, 1082 cells |
| GSM2741426 |
Trachea 1wk post-injury by polidocanol, mouse id 67, 1068 cells |
| GSM2741427 |
Trachea 1wk post-injury by polidocanol, mouse id 68, 1041 cells |
| GSM2741428 |
Trachea 1wk post-injury by polidocanol, mouse id 69, 212 cells |
| GSM2741429 |
HBECs donor 1, 1212 cells |
| GSM2741430 |
HBECs donor 2, 572 cells |
| GSM2741431 |
HBECs donor 3, 1186 cells |
| GSM3083199 |
HBECs transduced with GFP |
| GSM3083200 |
HBECs transduced with GFP:FOXI1 |
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| Relations |
| SRA |
SRP114254 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE102580_RAW.tar |
300.1 Mb |
(http)(custom) |
TAR (of TSV) |
| GSE102580_filtered_normalized_counts_human.tsv.gz |
58.9 Mb |
(ftp)(http) |
TSV |
| GSE102580_filtered_normalized_counts_human_viral_transduction.tsv.gz |
326.5 Mb |
(ftp)(http) |
TSV |
| GSE102580_filtered_normalized_counts_mouse.tsv.gz |
249.2 Mb |
(ftp)(http) |
TSV |
| GSE102580_meta_filtered_counts_human.tsv.gz |
115.2 Kb |
(ftp)(http) |
TSV |
| GSE102580_meta_filtered_counts_human_viral_transduction.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
| GSE102580_meta_filtered_counts_mouse.tsv.gz |
749.7 Kb |
(ftp)(http) |
TSV |
| GSE102580_meta_raw_counts_human.tsv.gz |
892.0 Kb |
(ftp)(http) |
TSV |
| GSE102580_meta_raw_counts_human_viral_transduction.tsv.gz |
3.3 Mb |
(ftp)(http) |
TSV |
| GSE102580_meta_raw_counts_mouse.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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