|
| Status |
Public on Mar 09, 2022 |
| Title |
Emphysema_ControlElastase_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Lung
group: Emphysema_ControlElastase
age: post-elastase day 21
genotype: wild type
|
| Treatment protocol |
Nicotine (200 mg/L) was started immediately after mating and administered to the females in drinking water supplemented with 2% saccharin for the whole period of gestation and lactation. As a control, we used drinking water with 2% saccharin. Pups born from nicotine-exposed mothers (nicotine group) or the controls (control group) were instilled intranasaly either with elastase or saline at the age of 11 weeks and their lungs were harvested at post-elastase day (ped) 21 for further RNAseq analysis.
|
| Growth protocol |
C57BL/6J mice, obtained from the mice facility of University of Geneva were kept under specific-pathogen-free conditions. Housing conditions were 12 hours day and 12 hours night. Mice had access to food and drinking water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Offspring lungs were collected at ped21 and laser dissected and 3-5 mouse lungs were used for each group (C-S, N-S, eC-E, nC-E, eN-E, nN-E). cDNA libraries were constructed by the Genomic platform of the University of Geneva using the Illumina TruSeq RNA Sample Preparation Kit (CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq. Smarter + Nextera technology was used due to low initial levels of mRNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Raw reads were all trimmed to 50bp and mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Raw_counts.txt
|
| |
|
| Submission date |
Feb 25, 2021 |
| Last update date |
Mar 09, 2022 |
| Contact name |
Sylvain LEMEILLE |
| Organization name |
University of Geneva Medical School
|
| Department |
Department of Pathology and Immunology
|
| Street address |
1 rue Michel-Servet
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE167568 |
Effect of in utero nicotine exposure and elastase instillation on transcriptomic profile at post-elastase day 21 in mice |
| GSE167569 |
Lung genes modification in elastase-induced emphysema following in utero nicotine exposure |
|
| Relations |
| BioSample |
SAMN18059594 |
| SRA |
SRX10171068 |
