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Sample GSM2656169

Query DataSets for GSM2656169

Status

Public on Jun 01, 2020

Title

Sample type

SRA

Source name

tracheal carina

Organism

Sus scrofa

Characteristics

genotype: CFTR+/+
infection: Non infected
Sex: M
tissue: tracheal carina

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.

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.

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.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

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.

Submission date

Jun 09, 2017

Last update date

Jun 01, 2020

Contact name

Kevin Lebrigand

Organization name

IPMC/CNRS

Lab

Functional Genomics Platform of Nice-Sophia-Antipolis, France.

Street address

660 route des lucioles