Refer to Data Download for additional information.
Manuscript: https://www.nature.com/articles/s41467-023-36352-z
Epithelial tissues provide front-line barriers shielding the organism from invading pathogens and harmful substances. In the airway epithelium, the combined action of multiciliated and secretory cells sustains the mucociliary escalator required for clearance of microbes and particles from the airways. Defects in components of mucociliary clearance or barrier integrity are associated with recurring infections and chronic inflammation. The timely and balanced differentiation of basal cells into mature epithelial cell subsets is therefore tightly controlled. While different growth factors regulating progenitor cell proliferation have been described, little is known about the role of metabolism in these regenerative processes. Here we show that basal cell differentiation correlates with a shift in cellular metabolism from glycolysis to fatty acid oxidation (FAO). We demonstrate both in vitro and in vivo that pharmacological and genetic impairment of FAO blocks the development of fully differentiated airway epithelial cells, compromising the repair of airway epithelia. Mechanistically, FAO links to the hexosamine biosynthesis pathway to support protein glycosylation in airway epithelial cells. Our findings unveil the metabolic network underpinning the differentiation of airway epithelia and identify novel targets for intervention to promote lung repair.
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Public data: https://www.ebi.ac.uk/ena/browser/view/PRJNA862107
In the ‘view search box' enter one of the following identifiers:
Project accession: PRJNA862107
Once there, you can download any associated files by clicking the relevant links and then clicking on “Get download script”.
| Code Block |
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wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/072/SRR20622172/SRR20622172.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/073/SRR20622173/SRR20622173.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/077/SRR20622177/SRR20622177.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/076/SRR20622176/SRR20622176.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/080/SRR20622180/SRR20622180.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/074/SRR20622174/SRR20622174.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/078/SRR20622178/SRR20622178.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/079/SRR20622179/SRR20622179.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/075/SRR20622175/SRR20622175.fastq.gz |
Now create a PBS Pro submission script for the above and save it in a file called, for example ‘launch_ENA_download.pbs’. Note: the below script will download the data in the folder from where the script has been sent to the cluster.
| Code Block |
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#!/bin/bash -l
#PBS -N ENA_download
#PBS -l select=1:ncpus=2:mem=8gb
#PBS -l walltime=24:00:00
#work on current directory (folder)
cd $PBS_O_WORKDIR
#copy and paste below the content of the ENA download script
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/072/SRR20622172/SRR20622172.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/073/SRR20622173/SRR20622173.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/077/SRR20622177/SRR20622177.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/076/SRR20622176/SRR20622176.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/080/SRR20622180/SRR20622180.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/074/SRR20622174/SRR20622174.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/078/SRR20622178/SRR20622178.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/079/SRR20622179/SRR20622179.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/075/SRR20622175/SRR20622175.fastq.gz |
Submit the download script to the cluster:
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qsub launch_ENA_download.pbs |
Monitor progress of job:
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qjobs |