|
| Status |
Public on May 21, 2022 |
| Title |
ALI_DMSO_Flagellin_24h_2 |
| Sample type |
SRA |
| |
|
| Source name |
Pig bronchial epithelial cells
|
| Organism |
Sus scrofa |
| Characteristics |
cell type: Bronchial epithelial cells differentiated under air-liquid condition
genotype: Wild type
age: 1 month
treatment 1: DMSO for 1h
treatment 2: 100 ng/ml Flagellin for 24 h
|
| Treatment protocol |
20 µM SB203580 or the vehicle (DMSO) for 1 h and then 100 ng/ml Flagellin or not (PBS) for 2 h or 24 h.
|
| Growth protocol |
Epithelial cells were dissected from the bronchi 1-month-old pigs by enzymatic digestion (0.1% proteases mix and 0.01% deoxyribonuclease I) during 24h at 4°C. The enzymatic digestion was stopped by the addition of a 10% volume of foetal bovine serum and cells were recovered and seeded onto 0.4 μm semi-permeable membranes (Greiner bio-one, Les Ulis, France) treated with collagen type 1. Cells were cultured until confluency and then cultured in an air-liquid-interface (ALI) at 37°C in 5% CO2 atmosphere. Culture medium was DMEM/F12 supplemented with SupplementMix (PromoCell C-39165), Glutamine (2 mM) and penicillin/streptomycin (100U/µg/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Paired-end
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Preincubated 1h DMSO, 100 ng/ml Flagellin for 24 h.
|
| Data processing |
STAR_2.4.0a paired-end mapping versus Sscrofa11.2.
FeatureCounts transcripts quantification (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Sus_Crofa.GRCm38.77 Ensembl GTF annotation file.
Genome_build: Sscrofa11.2
Supplementary_files_format_and_content: featurecounts.txt: Tab-delimited text file; Feature Counts.
|
| |
|
| Submission date |
May 03, 2021 |
| Last update date |
May 21, 2022 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL20983 |
| Series (1) |
| GSE173768 |
Airway administration of flagellin regulates the inflammatory response to Pseudomonas aeruginosa |
|
| Relations |
| BioSample |
SAMN18987109 |
| SRA |
SRX10760225 |
