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| Status |
Public on Jul 30, 2024 |
| Title |
Cell culture differentiation and proliferation conditions influence the in vitro regeneration of the human airway epithelium |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The human airway mucociliary epithelium can be recapitulatedin vitro using primary cells cultured in an Air-Liquid Interface (ALI), a reliable surrogate to perform pathophysiological studies. As tremendous variations exist between media used for ALI-cultured human airway epithelial cells, our study aimed to evaluate at a single-cell level the impact of several media (e.g. BEGMTM, PneumaCultTM, “Half&Half” and “Clancy”) on cell type distribution. Our work revealed the impact of these media on cell composition, gene expression profile, cell signaling or epithelial shape. We also established that proliferation in PneumaCultTM-Ex Plus favored secretory cells fate, showing the key influence of proliferation media on late differentiation epithelial characteristics. Altogether, our data offer a comprehensive repertoire for evaluating the effects of culture conditions on airway epithelial differentiation and will help to choose the most relevant medium according to the phenomenon to be investigated such as cilia or mucus biology or viral infection. We detail useful parameters that should be explored to document airway epithelial cell fate and shaping.
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| Overall design |
The study here generated single-cell dataset of human airways after in vitro regeneration at the Air-Liquid Interface. Samples from 2 donors were used for the establishment of Human Bronchial Epithelial Cell cultures (HBECs) and were analyzed during proliferation, at the onset of differentiation (ALI0) and after full differentiation (ALI28), in 4 distinct culture media. Single-cell RNAseq was performed with 10x v2 using hashtag antibodies for multiplexing, and sequenced on a NextSeq 500. Samples from 3 additional donors were used for the establishment of Human Nasal Epithelial Cell cultures (HNECs) and were analyzed during proliferation in three distinct culture media. Single-cell RNAseq was performed with 10x v2 without multiplexing, and sequenced on a NextSeq 2000. Raw data has been submitted to EGA web portal under accession number EGAS00001007572 (https://ega-archive.org/studies/EGAS00001007572).
Note from submitter: we uploaded the raw data at the European Genome-Phenome Archive (EGA) as required by our consortium policy (Human Cell Atlas) under accession number : EGAS00001007572.
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| Contributor(s) |
Redman E, Fierville M, Cavard A, Arguel M, Ruiz Garcia S, Girard C, Lebrigand K, Barbry P, Marcet B, Zaragosi L |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Sep 13, 2023 |
| Last update date |
Jul 31, 2024 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
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| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
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| Street address |
660 route des lucioles
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| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL30173 |
NextSeq 2000 (Homo sapiens) |
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| Samples (11)
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| GSM7777874 |
Prolif,HBECS,Donor1 |
| GSM7777875 |
Prolif,HBECS,Donor2 |
| GSM7777876 |
Prolif,HNECS,PneumaExPlus,Donor467 |
| GSM7777877 |
Prolif,HNECS,BEGM,Donor467 |
| GSM7777878 |
Prolif,HNECS,PneumaExPlus,Donor543 |
| GSM7777879 |
Prolif,HNECS,PneumaEx,Donor543 |
| GSM7777880 |
Prolif,HNECS,PneumaExPlus,Donor538 |
| GSM7777881 |
Prolif,HNECS,PneumaEx,Donor538 |
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| Relations |
| BioProject |
PRJNA1016280 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE243045_RAW.tar |
591.0 Mb |
(http)(custom) |
TAR (of TAR) |
| GSE243045_metadata.tsv.gz |
750 b |
(ftp)(http) |
TSV |
| GSE243045_readme.txt |
145 b |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
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