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| Status |
Public on Jun 01, 2020 |
| Title |
M12 |
| Sample type |
SRA |
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| Source name |
tracheal carina
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| Organism |
Sus scrofa |
| Characteristics |
genotype: CFTR-/-
infection: Non infected
Sex: M
tissue: tracheal carina
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| Treatment protocol |
Infection protocol: CFTR-/- and CFTR+/+ weighing 1 ± 0.2 kg were anesthetized with isoflurane (Vetflurane®). The trachea of each pig was then intubated and ventilated mechanically with a Fabius® Tiro® Ventilator (Dräger, Telford, USA). The ventilator settings were: volume controlled mode, tidal volume = 8-10 mL.kg-1, positive end-expiratory pressure = 5 cmH2O, respiratory rate = 15 breath.min-1, and inspiratory/expiratory ratio = 0.5, 50% oxygen in air. Piglets were inoculated with 2 mL of a suspension of luminescent P. aeruginosa strain PAKlux (5 x 10^6 cfu/mL) into the carina of trachea using an esophageal probe. Piglets were ventilated mechanically and monitored during the whole procedure and sacrificed 6 hours after infection.
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| Growth protocol |
All experiments were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee at INRA. The protocol was approved by the French “Ministère de l’éducation nationale, de l’enseignement supérieur et de la recherche” (n° 1166-2015071615392426). Male and female CFTR+/- transgenic pigs were provided by the LMU Munich, Germany (Klymiuk, Mundhenk et al., 2012), transferred to INRA, Nouzilly (France) and mated to generate CFTR+/+, CFTR+/- and CFTR-/- (CF) piglets. Piglets were allowed to suckle colostrum and genotype was confirmed by multiplex PCR as described below. All experiments were performed within 12 hours of birth. Non-infected newborn piglets were sacrificed by electronarcosis followed by exsanguination in the experimental slaughterhouse. Newborn piglets infected by P. aeruginosa were sacrificed by an i.v. overdose of pentobarbital (Dolethal, Vétoquinol, France) and exsanguinated before collection of post-mortem samples.
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| Extracted molecule |
total RNA |
| Extraction protocol |
1 µg of total RNA were depleted from ribosomal RNA with the Ribozero kit (Illumina Kit)
Illumina TruSeq Stranded Total RNA Sample Preparation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Mapping with STAR_2.4.0a versus Sscrofa10.2 and Pseudomonas_aeruginosa_PAK_518 genome
Read counting with featureCounts (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options
Statistical analysis performed on Sus scrofa genes only. Genes which did not have at least 5 counts in at least 2 samples were filtered out.
Normalization performed with DESeq2
Genome_build: Scrofa10.2
Supplementary_files_format_and_content: Matrix of normalized counts with genes as rows and sample as columns.
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| Submission date |
Jun 09, 2017 |
| Last update date |
Jun 01, 2020 |
| 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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| Platform ID |
GPL20983 |
| Series (1) |
| GSE99862 |
Early defects of airway mucin sialylation and of mucociliary clearance at the onset of lung pathogenesis in a pig model of cystic fibrosis |
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| Relations |
| BioSample |
SAMN07209359 |
| SRA |
SRX2899299 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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